1. MSstatsShiny
  2. Commit ab7f81fbb34a7fa2775e23485eba20f88b04749a
Browse code

Merge pull request #74 from Vitek-Lab/main

Bioc bug fix

Devon Kohler authored on 08/09/2023 15:00:14 • GitHub committed on 08/09/2023 15:00:14
Showing 10 changed files
R/module-loadpage-server.R
History View file @ ab7f81f
... ... 
@@ -12,70 +12,55 @@ loadpageServer <- function(id, parent_session) {
12 12 
   moduleServer(id, function(input, output, session) {
13 13 
     # toggle ui (DDA DIA SRM)
14 14 
     observe({
15 
-      if (input$DDA_DIA == "DDA") {
15 
+      print("bio")
16 
+
17 
+      print(input$BIO)
18 
+      if((input$BIO == "Protein" || input$BIO == "Peptide") && input$DDA_DIA == "LType"){
16 19 
         runjs("$('[type=radio][name=loadpage-filetype]:disabled').parent().parent().parent().find('div.radio').css('opacity', 1)")
17 20 
         enable("filetype")
18 
-        disable(selector = "[type=radio][value=spec]")
19 
-        disable(selector = "[type=radio][value=open]")
20 
-        disable(selector = "[type=radio][value=ump]")
21 21 
         disable(selector = "[type=radio][value=spmin]")
22 
-        disable(selector = "[type=radio][value=diann]")
23 22 
         runjs("$.each($('[type=radio][name=loadpage-filetype]:disabled'), function(_, e){ $(e).parent().parent().css('opacity', 0.4) })")
24 
-      }
25 
-      else if (input$DDA_DIA == "DIA") {
23 
+
24 
+      } else if ((input$BIO == "Protein" || input$BIO == "Peptide") && input$DDA_DIA == "TMT"){
26 25 
         runjs("$('[type=radio][name=loadpage-filetype]:disabled').parent().parent().parent().find('div.radio').css('opacity', 1)")
27 26 
         enable("filetype")
28 
-        disable(selector = "[type=radio][value=maxq]")
29 
-        disable(selector = "[type=radio][value=prog]")
30 
-        disable(selector = "[type=radio][value=PD]")
31 
-        disable(selector = "[type=radio][value=openms]")
32 
-        disable(selector = "[type=radio][value=spmin]")
33 
-        disable(selector = "[type=radio][value=phil]")
34 
-        runjs("$.each($('[type=radio][name=loadpage-filetype]:disabled'), function(_, e){ $(e).parent().parent().css('opacity', 0.4) })")
35 
-      }
36 
-      else if (input$DDA_DIA == "SRM_PRM") {
37 
-        runjs("$('[type=radio][name=loadpage-filetype]:disabled').parent().parent().parent().find('div.radio').css('opacity', 1)")
38 
-        enable("filetype")
39 
-        disable(selector = "[type=radio][value=maxq]")
27 
+        disable(selector = "[type=radio][value=sky]")
40 28 
         disable(selector = "[type=radio][value=prog]")
41 
-        disable(selector = "[type=radio][value=PD]")
42 
-        disable(selector = "[type=radio][value=openms]")
43 29 
         disable(selector = "[type=radio][value=spec]")
44 30 
         disable(selector = "[type=radio][value=open]")
45 31 
         disable(selector = "[type=radio][value=ump]")
46 
-        disable(selector = "[type=radio][value=spmin]")
47 
-        disable(selector = "[type=radio][value=phil]")
48 32 
         disable(selector = "[type=radio][value=diann]")
49 33 
         runjs("$.each($('[type=radio][name=loadpage-filetype]:disabled'), function(_, e){ $(e).parent().parent().css('opacity', 0.4) })")
50 
-      }
51 
-
52 
-      else if (input$DDA_DIA == "TMT") {
34 
+
35 
+      } else if (input$BIO == "PTM" && input$DDA_DIA == "LType"){
53 36 
         runjs("$('[type=radio][name=loadpage-filetype]:disabled').parent().parent().parent().find('div.radio').css('opacity', 1)")
54 37 
         enable("filetype")
55 
-        disable(selector = "[type=radio][value=sky]")
38 
+        # disable(selector = "[type=radio][value=sky]")
56 39 
         disable(selector = "[type=radio][value=prog]")
57 
-        disable(selector = "[type=radio][value=spec]")
40 
+        disable(selector = "[type=radio][value=PD]")
41 
+        disable(selector = "[type=radio][value=openms]")
42 
+        disable(selector = "[type=radio][value=spmin]")
58 43 
         disable(selector = "[type=radio][value=open]")
59 44 
         disable(selector = "[type=radio][value=ump]")
45 
+        disable(selector = "[type=radio][value=phil]")
60 46 
         disable(selector = "[type=radio][value=diann]")
61 
-        runjs("$.each($('[type=radio][name=loadpage-filetype]:disabled'), function(_, e){ $(e).parent().parent().css('opacity', 0.4) })")
62 47
63 
-      }
64 
-      else if (input$DDA_DIA %in% c("PTM", "PTM_TMT")) {
48 
+        runjs("$.each($('[type=radio][name=loadpage-filetype]:disabled'), function(_, e){ $(e).parent().parent().css('opacity', 0.4) })")
49 
+      }else if (input$BIO == "PTM" && input$DDA_DIA == "TMT"){
65 50 
         runjs("$('[type=radio][name=loadpage-filetype]:disabled').parent().parent().parent().find('div.radio').css('opacity', 1)")
66 51 
         enable("filetype")
67 
-        # disable(selector = "[type=radio][value=sky]")
68 52 
         disable(selector = "[type=radio][value=prog]")
69 
-        # disable(selector = "[type=radio][value=PD]")
70 53 
         disable(selector = "[type=radio][value=openms]")
71 
-        # disable(selector = "[type=radio][value=spec]")
54 
+        disable(selector = "[type=radio][value=spec]")
72 55 
         disable(selector = "[type=radio][value=open]")
73 56 
         disable(selector = "[type=radio][value=ump]")
74 57 
         disable(selector = "[type=radio][value=spmin]")
75 
-        # disable(selector = "[type=radio][value=phil]")
76 58 
         disable(selector = "[type=radio][value=diann]")
77 
-        runjs("$.each($('[type=radio][name=loadpage-filetype]:disabled'), function(_, e){ $(e).parent().parent().css('opacity', 0.4) })")
59 
+        disable(selector = "[type=radio][value=sky]")
60 
+
61 
+        runjs("$.each($('[type=radio][name=loadpage-filetype]:disabled'), function(_, e){ $(e).parent().parent().css('opacity', 0.4) })")
78 62 
       }
63 
+
79 64 
     })
80 65
81 66 
     observeEvent(input$filetype,{
... ... 
@@ -238,11 +223,11 @@ loadpageServer <- function(id, parent_session) {
238 223 
           h4("Summary of dataset"),
239 224 
           tableOutput(ns("summary2")),
240 225 
           tags$br(),
241 
-          conditionalPanel(condition = "input['loadpage-DDA_DIA'] !== 'PTM'",
226 
+          conditionalPanel(condition = "input['loadpage-BIO'] !== 'PTM'",
242 227 
                            h4("Top 6 rows of the dataset"),
243 228 
                            tableOutput(ns("summary"))
244 229 
           ),
245 
-          conditionalPanel(condition = "input['loadpage-DDA_DIA'] == 'PTM'",
230 
+          conditionalPanel(condition = "input['loadpage-BIO'] == 'PTM'",
246 231 
                            h4("Top 6 rows of the PTM dataset"),
247 232 
                            tableOutput(ns("summary_ptm")),
248 233 
                            tags$br(),
R/module-loadpage-ui.R
History View file @ ab7f81f
... ... 
@@ -52,15 +52,20 @@ loadpageUI <- function(id) {
52 52
53 53 
         # selection for DIA DDA or SRM/PRM
54 54
55 
+        radioButtons(ns("BIO"),
56 
+                     label <- h4("1. Biological Question",class = "icon-wrapper",icon("question-circle", lib = "font-awesome" ),
57 
+                                 div("Select the biological question of interest.", class = "icon-tooltip")),
58 
+                     c("Protein"="Protein", "Peptide"="Peptide","PTM"="PTM")
59 
+                     ),
55 60 
         radioButtons(ns("DDA_DIA"),
56 
-                     label <- h4("1. Experimental Design",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
57 
-                                 div("DDA/DIA/SRM/PRM are used for label-free preparation. PTM can either by label-free or TMT.", class = "icon-tooltip")),
58 
-                     c("DDA" = "DDA", "DIA" = "DIA", "SRM/PRM" = "SRM_PRM",
59 
-                       "DDA/TMT"="TMT", "PTM"="PTM")),
61 
+                     label <- h4("2. Label Type",class = "icon-wrapper",icon("question-circle", lib = "font-awesome" ),
62 
+                                 div("Label-free will process all label-free acquisitions including DDA/DIA/SRM/PRM.", class = "icon-tooltip")),
63 
+                     c("Label-Free"="LType", "TMT"="TMT")
64 
+        ),
60 65 
         # upload
61 66
62 67 
         radioButtons(ns("filetype"),
63 
-                     label <- h4("2. Type of File",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
68 
+                     label <- h4("3. Type of File",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
64 69 
                                  div("Choose the spectral processing tool used to process your data", class = "icon-tooltip")),
65 70 
                      choices = c("Example dataset" = "sample",
66 71 
                                  "MSstats Format" = "msstats",
... ... 
@@ -70,26 +75,21 @@ loadpageUI <- function(id) {
70 75 
                                  "OpenSWATH" = "open", "DIA-Umpire" = "ump",
71 76 
                                  "SpectroMine" = "spmin", "FragPipe" = "phil", "DIANN"="diann"),
72 77 
                      selected = character(0)),
73 
-        conditionalPanel(
74 
-          condition = "input['loadpage-DDA_DIA'] != 'PTM'",
75 
-          radioButtons(ns("level"),
76 
-                       label <- h4("3. Analysis Level",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
77 
-                                   div("Choose either peptide or protein level of analysis. MSstats is classically designed for protein level analysis and peptide analysis may produce inconsistent results.", class = "icon-tooltip")),
78 
-                       choices = c("Protein" = "Protein", "Peptide" = "Peptide"),
79 
-                       selected = "Protein")
80 
-        ),
78 
+
79 
+        tags$hr(),
80 
+        conditionalPanel( condition="input['loadpage-BIO'] != 'PTM' && input['loadpage-filetype'] == 'sample' && input['loadpage-DDA_DIA'] == 'LType' ",
81 
+                     radioButtons(ns("LabelFreeType"),
82 
+                     label <- h4("4. Type of Label-Free type",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
83 
+                                 div("Choose the spectral processing tool used to process your data", class = "icon-tooltip")),
84 
+                     choices = c("DDA" = "DDA",
85 
+                                 "DIA" ="DIA",
86 
+                                 "SRM/PRM" ="SRM_PRM"),
87 
+                     selected = character(0))),
88 
+
81 89 
         tags$hr(),
82 
-        conditionalPanel(
83 
-          condition = "input['loadpage-filetype'] == 'sample' && input['loadpage-DDA_DIA'] == 'PTM' && input['loadpage-filetype'] != 'phil'",
84 
-          radioButtons(ns("PTMTMT"),
85 
-                       label <- h4("3. TMT Experiment",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
86 
-                                   div("Indicate whether to use a label free or TMT sample experiment", class = "icon-tooltip")),
87 
-                       c(No='No', Yes='Yes'),
88 
-                       inline=TRUE)
89 
-        ),
90 90 
         conditionalPanel(
91 91 
           condition = "(input['loadpage-filetype'] =='10col' || input['loadpage-filetype'] =='prog' || input['loadpage-filetype'] =='PD' || input['loadpage-filetype'] =='open'||
92 
-                   input['loadpage-filetype'] =='openms' || input['loadpage-filetype'] =='spmin' || input['loadpage-filetype'] == 'phil') && input['loadpage-DDA_DIA'] != 'PTM'",
92 
+                   input['loadpage-filetype'] =='openms' || input['loadpage-filetype'] =='spmin' || input['loadpage-filetype'] == 'phil') && input['loadpage-BIO'] != 'PTM'",
93 93 
           h4("4. Upload quantification dataset"),
94 94 
           fileInput(ns('data'), "", multiple = FALSE,
95 95 
                     accept = c("text/csv",
... ... 
@@ -101,7 +101,7 @@ loadpageUI <- function(id) {
101 101 
                        c(Comma=",",Semicolon=";", Tab="\t",Pipe="|"),
102 102 
                        inline = TRUE)
103 103 
         ),
104 
-        conditionalPanel(condition = "input['loadpage-filetype'] == 'msstats' && input['loadpage-DDA_DIA'] != 'PTM' && input['loadpage-DDA_DIA'] != 'PTM_TMT'",
104 
+        conditionalPanel(condition = "input['loadpage-filetype'] == 'msstats' && (input['loadpage-BIO'] != 'PTM' && (input['loadpage-BIO'] != 'PTM' && input['loadpage-DDA_DIA'] != 'TMT'))",
105 105 
                          h4("4. Upload data in MSstats Format"),
106 106 
                          fileInput(ns('msstatsdata'), "", multiple = FALSE,
107 107 
                                    accept = c("text/csv",
... ... 
@@ -113,7 +113,7 @@ loadpageUI <- function(id) {
113 113 
                                       c(Comma=",",Semicolon=";", Tab="\t",Pipe="|"),
114 114 
                                       inline = TRUE)
115 115 
         ),
116 
-        conditionalPanel(condition = "input['loadpage-filetype'] == 'msstats' && (input['loadpage-DDA_DIA'] == 'PTM' || input['loadpage-DDA_DIA'] == 'PTM_TMT')",
116 
+        conditionalPanel(condition = "input['loadpage-filetype'] == 'msstats' && (input['loadpage-BIO'] == 'PTM' || (input['loadpage-BIO'] == 'PTM' && input['loadpage-DDA_DIA'] == 'TMT'))",
117 117 
                          h4("4. Upload PTM data in MSstats Format"),
118 118 
                          fileInput(ns('msstatsptmdata'), "", multiple = FALSE,
119 119 
                                    accept = c("text/csv",
... ... 
@@ -125,7 +125,7 @@ loadpageUI <- function(id) {
125 125 
                                       c(Comma=",",Semicolon=";", Tab="\t",Pipe="|"),
126 126 
                                       inline = TRUE)
127 127 
         ),
128 
-        conditionalPanel(condition = "input['loadpage-filetype'] == 'sky' && input['loadpage-DDA_DIA'] != 'PTM'",
128 
+        conditionalPanel(condition = "input['loadpage-filetype'] == 'sky' && input['loadpage-BIO'] != 'PTM'",
129 129 
                          h4("4. Upload MSstats report from Skyline"),
130 130 
                          fileInput(ns('skylinedata'), "", multiple = FALSE,
131 131 
                                    accept = c("text/csv",
... ... 
@@ -137,7 +137,7 @@ loadpageUI <- function(id) {
137 137 
                                       c(Comma=",",Semicolon=";", Tab="\t",Pipe="|"),
138 138 
                                       inline = TRUE)
139 139 
         ),
140 
-        conditionalPanel(condition = "input['loadpage-filetype'] == 'diann' && input['loadpage-DDA_DIA'] != 'PTM'",
140 
+        conditionalPanel(condition = "input['loadpage-filetype'] == 'diann' && input['loadpage-BIO'] != 'PTM'",
141 141 
                          h4("4. Upload MSstats report from DIANN"),
142 142 
                          fileInput(ns('dianndata'), "", multiple = FALSE,
143 143 
                                    accept = c("text/csv",
... ... 
@@ -149,7 +149,7 @@ loadpageUI <- function(id) {
149 149 
                                       c(Comma=",",Semicolon=";", Tab="\t",Pipe="|"),
150 150 
                                       inline = TRUE)
151 151 
         ),
152 
-        conditionalPanel(condition = "input['loadpage-filetype'] == 'spec' && input['loadpage-DDA_DIA'] != 'PTM'",
152 
+        conditionalPanel(condition = "input['loadpage-filetype'] == 'spec' && input['loadpage-BIO'] != 'PTM'",
153 153 
                          h4("4. Upload MSstats scheme output from Spectronaut"),
154 154 
                          fileInput(ns('specdata'), "", multiple = FALSE,
155 155 
                          accept = c("text/csv",".xlsx",
... ... 
@@ -171,7 +171,7 @@ loadpageUI <- function(id) {
171 171 
         # ),
172 172
173 173 
         conditionalPanel(
174 
-          condition = "input['loadpage-filetype'] == 'phil' && input['loadpage-DDA_DIA'] == 'PTM'",
174 
+          condition = "input['loadpage-filetype'] == 'phil' && input['loadpage-BIO'] == 'PTM'",
175 175 
           h4("3. Upload PTM msstats dataset"),
176 176 
           fileInput(ns('ptmdata'), "", multiple = FALSE,
177 177 
                     accept = c("text/csv",
... ... 
@@ -206,13 +206,13 @@ loadpageUI <- function(id) {
206 206 
         ),
207 207
208 208
209 
-        conditionalPanel(condition = "(input['loadpage-filetype'] == 'spec' || input['loadpage-filetype'] =='spmin') && input['loadpage-DDA_DIA'] != 'PTM'",
209 
+        conditionalPanel(condition = "(input['loadpage-filetype'] == 'spec' || input['loadpage-filetype'] =='spmin') && input['loadpage-BIO'] != 'PTM'",
210 210 
                          fileInput(ns('data1'), "", multiple = FALSE, accept = c(".xls")),
211 211 
         ),
212 212 
         tags$br(),
213 213 
         conditionalPanel(
214 
-          condition = "(input['loadpage-filetype'] == 'sky' || input['loadpage-filetype'] == 'prog' || input['loadpage-filetype'] == 'PD' || input['loadpage-filetype'] == 'spec' || input['loadpage-filetype'] == 'open'|| input['loadpage-filetype'] =='spmin' || input['loadpage-filetype'] == 'phil' || input['loadpage-filetype'] == 'diann') && input['loadpage-DDA_DIA'] != 'PTM'",
215 
-          h4("5. Upload annotation Filel", class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
214 
+          condition = "(input['loadpage-filetype'] == 'sky' || input['loadpage-filetype'] == 'prog' || input['loadpage-filetype'] == 'PD' || input['loadpage-filetype'] == 'spec' || input['loadpage-filetype'] == 'open'|| input['loadpage-filetype'] =='spmin' || input['loadpage-filetype'] == 'phil' || input['loadpage-filetype'] == 'diann') && input['loadpage-BIO'] != 'PTM'",
215 
+          h4("5. Upload annotation File", class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
216 216 
                                                  div("Upload manually created annotation file. This file maps MS runs to experiment metadata (i.e. conditions, bioreplicates). Please see Help tab for information on creating this file.",class = "icon-tooltip")),
217 217 
            #downloadLink("template", "Annotation file template"),
218 218 
           fileInput(ns('annot'), "", multiple = FALSE,
... ... 
@@ -221,34 +221,30 @@ loadpageUI <- function(id) {
221 221 
         ),
222 222 
         tags$br(),
223 223 
         ## PTM Fragpipe input -- --------------------------------------------------------
224 
-        conditionalPanel(condition = "input['loadpage-filetype'] == 'msstats' && (input['loadpage-DDA_DIA'] == 'PTM' || input['loadpage-DDA_DIA'] == 'PTM_TMT')",
224 
+        conditionalPanel(condition = "input['loadpage-filetype'] == 'msstats' && (input['loadpage-BIO'] == 'PTM' || (input['loadpage-BIO'] == 'PTM' && input['loadpage-DDA_DIA'] == 'TMT'))",
225 225 
                          h4("4. (Optional) Upload unmodified data in MSstats Format"),
226 226 
                          fileInput(ns('unmod'), "", multiple = FALSE,
227 227 
                                    accept = c("text/csv",
228 228 
                                               "text/comma-separated-values,text/plain",
229 229 
                                               ".csv")),
230 
-                         tags$br(),
231 
-                         radioButtons(ns("PTMTMT"),
232 
-                                      label = h4("5. TMT Experiment", class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
233 
-                                                 div("Indicate if experiment was processed using TMT labeling",class = "icon-tooltip")),
234 
-                                      c(No='No', Yes='Yes'),
235 
-                                      inline = TRUE)),
230 
+                         tags$br()
231 
+                         ),
236 232 
         conditionalPanel(
237 
-          condition = "input['loadpage-filetype'] == 'maxq' && (input['loadpage-DDA_DIA'] != 'PTM' && input['loadpage-DDA_DIA'] != 'PTM_TMT')",
238 
-          h4("5. Upload evidence.txt File"),
233 
+          condition = "input['loadpage-filetype'] == 'maxq' && input['loadpage-BIO'] != 'PTM' && (input['loadpage-DDA_DIA'] == 'TMT' || input['loadpage-DDA_DIA'] == 'LType')",
234 
+          h4("4. Upload evidence.txt File"),
239 235 
           fileInput(ns('evidence'), "", multiple = FALSE,
240 236 
                     accept = c("text/csv", "text/comma-separated-values,text/plain", ".csv")),
241 
-          h4("6. Upload proteinGroups.txt File"),
237 
+          h4("5. Upload proteinGroups.txt File"),
242 238 
           fileInput(ns('pGroup'), "", multiple = FALSE,
243 239 
                     accept = c("text/csv", "text/comma-separated-values,text/plain", ".csv")),
244 
-          h4("7. Upload annotation File", class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
240 
+          h4("6. Upload annotation File", class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
245 241 
                                                  div("Upload manually created annotation file. This file maps MS runs to experiment metadata (i.e. conditions, bioreplicates). Please see Help tab for information on creating this file.",class = "icon-tooltip")),
246 242 
           fileInput(ns('annot1'), "", multiple = FALSE,
247 243 
                     accept = c("text/csv", "text/comma-separated-values,text/plain", ".csv"))
248 244 
         ),
249 245 
         ## PTM input -- --------------------------------------------------------
250 246 
         conditionalPanel(
251 
-          condition = "(input['loadpage-filetype'] == 'maxq' || input['loadpage-filetype'] == 'PD' || input['loadpage-filetype'] == 'spec' || input['loadpage-filetype'] == 'sky') && (input['loadpage-DDA_DIA'] == 'PTM' || input['loadpage-DDA_DIA'] == 'PTM_TMT')",
247 
+          condition = "(input['loadpage-filetype'] == 'maxq' || input['loadpage-filetype'] == 'PD' || input['loadpage-filetype'] == 'spec' || input['loadpage-filetype'] == 'sky') && (input['loadpage-BIO'] == 'PTM' || (input['loadpage-BIO'] == 'PTM' && input['loadpage-DDA_DIA'] == 'TMT'))",
252 248 
           h4("4. Upload PTM input.txt File"),
253 249 
           fileInput(ns('ptm_input'), "", multiple = FALSE,
254 250 
                     accept = c("text/csv",".xlsx",
... ... 
@@ -267,38 +263,32 @@ loadpageUI <- function(id) {
267 263 
                     accept = c("text/csv/xlsx", "text/comma-separated-values,text/plain", ".csv", ".xlsx"))
268 264 
         ),
269 265 
         conditionalPanel(
270 
-          condition = "(input['loadpage-filetype'] == 'maxq') && (input['loadpage-DDA_DIA'] == 'PTM' || input['loadpage-DDA_DIA'] == 'PTM_TMT')",
266 
+          condition = "(input['loadpage-filetype'] == 'maxq') && (input['loadpage-BIO'] == 'PTM' || (input['loadpage-BIO'] == 'PTM' && input['loadpage-DDA_DIA'] == 'TMT'))",
271 267 
           h4("7. (Optional) Upload Unmodified Protein proteinGroups.txt File"),
272 268 
           fileInput(ns('ptm_pgroup'), "", multiple = FALSE,
273 269 
                     accept = c("text/csv", "text/comma-separated-values,text/plain", ".csv"))
274 270 
         ),
271 
+
275 272 
         conditionalPanel(
276 
-          condition = "(input['loadpage-filetype'] == 'maxq' || input['loadpage-filetype'] == 'PD') && (input['loadpage-DDA_DIA'] == 'PTM' || input['loadpage-DDA_DIA'] == 'PTM_TMT')",
277 
-          radioButtons(ns("PTMTMT_maxq_pd"),
278 
-                       label = h4("TMT Experiment", class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
279 
-                                  div("Indicate if experiment was processed using TMT labelin",class = "icon-tooltip")),
280 
-                       c(No='No', Yes='Yes'),
281 
-                       selected='Yes',inline = TRUE)),
282 
-        conditionalPanel(
283 
-          condition = "(input['loadpage-filetype'] == 'maxq') && (input['loadpage-DDA_DIA'] == 'PTM' || input['loadpage-DDA_DIA'] == 'PTM_TMT')",
273 
+          condition = "(input['loadpage-filetype'] == 'maxq') && (input['loadpage-BIO'] == 'PTM' || (input['loadpage-BIO'] == 'PTM' && input['loadpage-DDA_DIA'] == 'TMT'))",
284 274 
           h4("Modification Label",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),div("Indicate if experiment was processed using TMT labeling",class = "icon-tooltip")),
285 275 
           textInput(ns("mod_id_maxq"), "",
286 276 
                     value="\\(Phospho \\(STY\\)\\)")
287 277 
         ),
288 278 
         conditionalPanel(
289 
-            condition = "(input['loadpage-filetype'] == 'PD') && (input['loadpage-DDA_DIA'] == 'PTM' || input['loadpage-DDA_DIA'] == 'PTM_TMT')",
279 
+            condition = "(input['loadpage-filetype'] == 'PD') && (input['loadpage-BIO'] == 'PTM' || (input['loadpage-BIO'] == 'PTM' && input['loadpage-DDA_DIA'] == 'TMT'))",
290 280 
             h4("Modification Label", class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),div("Indicate if experiment was processed using TMT labeling",class = "icon-tooltip")),
291 281 
             textInput(ns("mod_id_pd"), "",
292 282 
                          value="\\(Phospho\\)")
293 283 
         ),
294 284 
         conditionalPanel(
295 
-          condition = "(input['loadpage-filetype'] == 'spec') && (input['loadpage-DDA_DIA'] == 'PTM' || input['loadpage-DDA_DIA'] == 'PTM_TMT')",
285 
+          condition = "(input['loadpage-filetype'] == 'spec') && (input['loadpage-BIO'] == 'PTM' || (input['loadpage-BIO'] == 'PTM' && input['loadpage-DDA_DIA'] == 'TMT'))",
296 286 
           h4("Modification Label",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),div("Indicate if experiment was processed using TMT labeling",class = "icon-tooltip")),
297 287 
           textInput(ns("mod_id_spec"),"",
298 288 
                     value="\\[Phospho \\(STY\\)\\]")
299 289 
         ),
300 290 
         conditionalPanel(
301 
-          condition = "(input['loadpage-filetype'] == 'maxq' || input['loadpage-filetype'] == 'PD' || input['loadpage-filetype'] == 'spec' || input['loadpage-filetype'] == 'sky') && (input['loadpage-DDA_DIA'] == 'PTM' || input['loadpage-DDA_DIA'] == 'PTM_TMT')",
291 
+          condition = "(input['loadpage-filetype'] == 'maxq' || input['loadpage-filetype'] == 'PD' || input['loadpage-filetype'] == 'spec' || input['loadpage-filetype'] == 'sky') && (input['loadpage-BIO'] == 'PTM' || (input['loadpage-BIO'] == 'PTM' && input['loadpage-DDA_DIA'] == 'TMT'))",
302 292 
           h4("FASTA file column name",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),div("Name of column in FASTA file that matches with Protein name column in input. It is critical the values in both columns match so that the modfication can be identified.",class = "icon-tooltip")),
303 293 
           textInput(ns("mod_id_spec"),"",
304 294 
                     value="uniprot_iso")
... ... 
@@ -340,12 +330,12 @@ loadpageUI <- function(id) {
340 330 
         #                                                         title = "Enter the column in your data containing protein names")),
341 331 
         #                            value = "ProteinAccessions")),
342 332
343 
-        conditionalPanel(condition = "input['loadpage-filetype'] && input['loadpage-DDA_DIA'] == 'DDA' && input['loadpage-filetype'] !== 'sample' && input['loadpage-filetype'] !== 'MRF'",
333 
+        conditionalPanel(condition = "input['loadpage-filetype'] && input['loadpage-DDA_DIA'] == 'LType' && input['loadpage-filetype'] !== 'sample' && input['loadpage-filetype'] !== 'MRF'",
344 334 
                          h4("Select the options for pre-processing"),
345 335 
                          checkboxInput(ns("uniqe_peptides"), "Use unique peptides", value = TRUE),
346 336 
                          checkboxInput(ns("remove"), "Remove proteins with 1 peptide and charge", value = FALSE)),
347 337
348 
-        conditionalPanel(condition = "input['loadpage-filetype'] && input['loadpage-DDA_DIA'] == 'DIA' && input['loadpage-filetype'] !== 'sample'",
338 
+        conditionalPanel(condition = "input['loadpage-filetype'] && input['loadpage-DDA_DIA'] == 'LType' && input['loadpage-filetype'] !== 'sample'",
349 339 
                          checkboxInput(ns("remove"), "Remove proteins with 1 feature", value = FALSE),
350 340 
                          conditionalPanel(condition = "input['loadpage-filetype'] == 'sky' || input['loadpage-filetype'] == 'spec'|| input['loadpage-filetype'] == 'diann' ",
351 341 
                                           checkboxInput(ns("q_val"), "Filter with Q-value"),
R/module-qc-server.R
History View file @ ab7f81f
... ... 
@@ -27,7 +27,7 @@ qcServer <- function(input, output, session,parent_session, loadpage_input,get_d
27 27 
   output$Names = renderUI({
28 28 
     ns <- session$ns
29 29 
     if (input$standards == "Proteins") {
30 
-      if((loadpage_input()$DDA_DIA=="SRM_PRM" && loadpage_input()$filetype=="sky")||(loadpage_input()$DDA_DIA=="DIA" && loadpage_input()$filetype=="ump")){
30 
+      if((loadpage_input()$DDA_DIA=="LType" && loadpage_input()$filetype=="sky")||(loadpage_input()$DDA_DIA=="LType" && loadpage_input()$filetype=="ump")){
31 31
32 32 
         selectizeInput(ns("names"), "choose standard", unique(get_data()[2]), multiple = TRUE)
33 33 
       }
... ... 
@@ -80,7 +80,7 @@ qcServer <- function(input, output, session,parent_session, loadpage_input,get_d
80 80 
       #   m_feat = 20
81 81 
       #   }
82 82
83 
-      if (loadpage_input()$DDA_DIA =="PTM"){
83 
+      if (loadpage_input()$BIO =="PTM"){
84 84 
         m_feat = nrow(unique(get_data()$PTM[1]))
85 85 
       } else {
86 86 
         m_feat = nrow(unique(get_data()[1]))
... ... 
@@ -100,8 +100,10 @@ qcServer <- function(input, output, session,parent_session, loadpage_input,get_d
100 100
101 101 
   output$Which = renderUI({
102 102 
     ns <- session$ns
103 
-    if ((loadpage_input()$DDA_DIA!="PTM" && input$type1 == "QCPlot")) {
104 
-      if((loadpage_input()$DDA_DIA=="SRM_PRM" && input$filetype=="sky") || (loadpage_input()$DDA_DIA=="DIA" && loadpage_input()$filetype=="ump")){
103 
+    print("Inside render UI and getting input$type1")
104 
+    print(input$type1)
105 
+    if ((loadpage_input()$BIO!="PTM" && input$type1 == "QCPlot")) {
106 
+      if((loadpage_input()$DDA_DIA=="LType" && loadpage_input()$filetype=="sky") || (loadpage_input()$DDA_DIA=="LType" && loadpage_input()$filetype=="ump")){
105 107 
         selectizeInput(ns("which"), "Show plot for",
106 108 
                        choices = c("", "ALL PROTEINS" = "allonly",
107 109 
                                    unique(get_data()[2])))
... ... 
@@ -110,8 +112,8 @@ qcServer <- function(input, output, session,parent_session, loadpage_input,get_d
110 112 
                        choices = c("", "ALL PROTEINS" = "allonly",
111 113 
                                    unique(get_data()[1])))
112 114 
       }
113 
-    } else if (loadpage_input()$DDA_DIA == "PTM"){
114 
-      if (input$type1 == "QCPlot"){
115 
+    } else if (loadpage_input()$BIO == "PTM"){
116 
+      if (loadpage_input()$type1 == "QCPlot"){
115 117 
         selectizeInput(ns("which"), "Show plot for",
116 118 
                        choices = c("", "ALL PROTEINS" = "allonly",
117 119 
                                    unique(get_data()$PTM[1])))
... ... 
@@ -167,7 +169,7 @@ qcServer <- function(input, output, session,parent_session, loadpage_input,get_d
167 169 
                             address = file
168 170 
         )
169 171
170 
-      } else if (loadpage_input()$DDA_DIA == "PTM"){
172 
+      } else if (loadpage_input()$BIO == "PTM"){
171 173
172 174 
         dataProcessPlotsPTM(preprocess_data(),
173 175 
                             type=input$type1,
... ... 
@@ -247,7 +249,7 @@ qcServer <- function(input, output, session,parent_session, loadpage_input,get_d
247 249
248 250 
   observeEvent(input$run,{
249 251
250 
-    if(loadpage_input()$DDA_DIA=="PTM"){
252 
+    if(loadpage_input()$BIO=="PTM"){
251 253 
       enable("prepr_csv_ptm")
252 254 
       enable("summ_csv_ptm")
253 255 
       enable("prepr_csv_prot")
... ... 
@@ -417,7 +419,7 @@ qcServer <- function(input, output, session,parent_session, loadpage_input,get_d
417 419 
                                         type = input$typequant,
418 420 
                                         format = input$format,
419 421 
                                         use_log_file = FALSE)
420 
-    } else if (loadpage_input()$DDA_DIA == "PTM" & (loadpage_input()$PTMTMT == "Yes" | loadpage_input()$filetype=='phil')){
422 
+    } else if (loadpage_input()$BIO == "PTM" & ((loadpage_input()$BIO == "PTM" & loadpage_input()$DDA_DIA == "TMT") | loadpage_input()$filetype=='phil')){
421 423 
       temp = copy(preprocess_data())
422 424 
       setnames(temp$PTM$ProteinLevelData,
423 425 
                c("Abundance", "Condition", "BioReplicate"),
... ... 
@@ -426,7 +428,7 @@ qcServer <- function(input, output, session,parent_session, loadpage_input,get_d
426 428 
                                         type = input$typequant,
427 429 
                                         format = input$format,
428 430 
                                         use_log_file = FALSE)
429 
-    } else if (loadpage_input()$DDA_DIA == "PTM" & loadpage_input()$PTMTMT == "No"){
431 
+    } else if (loadpage_input()$BIO == "PTM" & (loadpage_input()$BIO == "PTM" & loadpage_input()$DDA_DIA != "TMT")){
430 432 
       temp = copy(preprocess_data())
431 433 
       abundant$results =quantification(temp$PTM,
432 434 
                                        type = input$typequant,
R/module-qc-ui.R
History View file @ ab7f81f
... ... 
@@ -22,12 +22,12 @@ qcUI <- function(id) {
22 22 
       tags$br(),
23 23 
       sidebarPanel(
24 24 
         # transformation
25 
-        conditionalPanel(condition = "input['loadpage-DDA_DIA'] == 'TMT' || (input['loadpage-DDA_DIA'] == 'PTM' && input['loadpage-PTMTMT'] == 'Yes')",
25 
+        conditionalPanel(condition = "input['loadpage-DDA_DIA'] == 'TMT' || (input['loadpage-BIO'] == 'PTM' && (input['loadpage-BIO'] == 'PTM' && input['loadpage-DDA_DIA'] == 'TMT'))",
26 26 
                          h4("1. Peptide level normalization",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
27 27 
                             div("Global median normalization on peptide level data, equalizes medians across all the channels and runs", class = "icon-tooltip")),
28 28 
                          checkboxInput(ns("global_norm"), "Yes", value = TRUE)),
29 29
30 
-        conditionalPanel(condition = "input['loadpage-DDA_DIA'] == 'SRM_PRM' || input['loadpage-DDA_DIA'] == 'DDA' || input['loadpage-DDA_DIA'] == 'DIA' || (input['loadpage-DDA_DIA'] == 'PTM' && input['loadpage-PTMTMT'] == 'No')",
30 
+        conditionalPanel(condition = "input['loadpage-DDA_DIA'] == 'LType' || (input['loadpage-BIO'] == 'PTM' && (input['loadpage-BIO'] == 'PTM' && input['loadpage-DDA_DIA'] != 'TMT'))",
31 31 
                          radioButtons(ns("log"),
32 32 
                                       label = h4("1. Log transformation",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
33 33 
                                                  div("Logarithmic transformation applied to the Intensity column", class = "icon-tooltip")),
... ... 
@@ -36,7 +36,7 @@ qcUI <- function(id) {
36 36
37 37 
         tags$hr(),
38 38
39 
-        conditionalPanel(condition = "input['loadpage-DDA_DIA'] == 'TMT' || (input['loadpage-DDA_DIA'] == 'PTM' && input['loadpage-PTMTMT'] == 'Yes')",
39 
+        conditionalPanel(condition = "input['loadpage-DDA_DIA'] == 'TMT' || (input['loadpage-BIO'] == 'PTM' && (input['loadpage-BIO'] == 'PTM' && input['loadpage-DDA_DIA'] == 'TMT'))",
40 40 
                          selectInput(ns("summarization"),
41 41 
                                      h4("2. Summarization method",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
42 42 
                                         div("Select method to be used for protein summarization. For details on each option please see Help tab", class = "icon-tooltip")),
... ... 
@@ -45,35 +45,35 @@ qcUI <- function(id) {
45 45 
                                        "Log(Sum)" = "LogSum","Median" = "Median"),
46 46 
                                      selected = "log")),
47 47
48 
-        conditionalPanel(condition = "(input['loadpage-DDA_DIA'] == 'TMT' || (input['loadpage-DDA_DIA'] == 'PTM' && input['loadpage-PTMTMT'] == 'Yes')) && input['qc-summarization'] == 'msstats'",
48 
+        conditionalPanel(condition = "(input['loadpage-DDA_DIA'] == 'TMT' || (input['loadpage-BIO'] == 'PTM' && (input['loadpage-BIO'] == 'PTM' && input['loadpage-DDA_DIA'] == 'TMT'))) && input['qc-summarization'] == 'msstats'",
49 49 
                          checkboxInput(ns("null"), label =tags$div("Do not apply cutoff",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
50 50 
                                           div("Maximum quantile for deciding censored missing values, default is 0.999", class = "icon-tooltip"))
51 51 
                                        ),
52 52 
                          numericInput(ns("maxQC"), NULL, 0.999, 0.000, 1.000, 0.001)),
53 53
54 54 
         # Normalization
55 
-        conditionalPanel(condition = "input['loadpage-DDA_DIA'] == 'SRM_PRM' || input['loadpage-DDA_DIA'] == 'DDA' || input['loadpage-DDA_DIA'] == 'DIA'",
55 
+        conditionalPanel(condition = "input['loadpage-DDA_DIA'] == 'LType'",
56 56 
                          selectInput(ns("norm"),
57 57 
                                      label = h4("2. Normalization",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
58 58 
                                         div("Normalization to remove systematic bias between MS runs. For more information visit the Help tab", class = "icon-tooltip")),
59 59 
                                      c("none" = "FALSE", "equalize medians" = "equalizeMedians",
60 60 
                                        "quantile" = "quantile", "global standards" = "globalStandards"),
61 61 
                                      selected = "equalizeMedians")),
62 
-        conditionalPanel(condition = "input['loadpage-DDA_DIA'] == 'PTM' && input['loadpage-PTMTMT'] == 'No'",
62 
+        conditionalPanel(condition = "input['loadpage-BIO'] == 'PTM' && (input['loadpage-BIO'] == 'PTM' && input['loadpage-DDA_DIA'] != 'TMT')",
63 63 
                          selectInput(ns("norm"),
64 64 
                                      label = h4("2. Normalization",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
65 65 
                                         div("Normalization to remove systematic bias between MS runs. For more information visit the Help tab", class = "icon-tooltip")),
66 66 
                                      c("none" = "FALSE", "equalize medians" = "equalizeMedians",
67 67 
                                        "quantile" = "quantile"),
68 68 
                                      selected = "equalizeMedians")),
69 
-        conditionalPanel(condition = "input['qc-norm'] == 'globalStandards' &&  (input['loadpage-DDA_DIA'] !== 'PTM' && input['loadpage-DDA_DIA'] !== 'TMT')",
69 
+        conditionalPanel(condition = "input['qc-norm'] == 'globalStandards' &&  (input['loadpage-BIO'] !== 'PTM' && input['loadpage-DDA_DIA'] !== 'TMT')",
70 70 
                          radioButtons(ns("standards"), "Choose type of standards",
71 71 
                                       c("Proteins", "Peptides")),
72 72 
                          uiOutput(ns("Names"))),
73 73 
         tags$hr(),
74 74
75 75 
         conditionalPanel(
76 
-          condition = "input['loadpage-DDA_DIA'] == 'TMT' || (input['loadpage-DDA_DIA'] == 'PTM' && input['loadpage-PTMTMT'] == 'Yes')",
76 
+          condition = "input['loadpage-DDA_DIA'] == 'TMT' || (input['loadpage-BIO'] == 'PTM' && (input['loadpage-BIO'] == 'PTM' && input['loadpage-DDA_DIA'] == 'TMT'))",
77 77 
           h4("3. Local protein normalization",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
78 78 
              div("Reference channel based normalization between MS runs on protein level data. Requires one reference channel in each MS run, annotated by 'Norm' in Condition column of annotation file", class = "icon-tooltip")),
79 79 
           checkboxInput(ns("reference_norm"), "Yes", value = TRUE),
... ... 
@@ -85,7 +85,7 @@ qcUI <- function(id) {
85 85
86 86
87 87 
         conditionalPanel(
88 
-          condition = "input['loadpage-DDA_DIA'] == 'DDA' || input['loadpage-DDA_DIA'] == 'DIA' || input['loadpage-DDA_DIA'] == 'SRM_PRM' || (input['loadpage-DDA_DIA'] == 'PTM' && input['loadpage-PTMTMT'] == 'No')",
88 
+          condition = "input['loadpage-DDA_DIA'] == 'LType'  || (input['loadpage-BIO'] == 'PTM' && (input['loadpage-BIO'] == 'PTM' && input['loadpage-DDA_DIA'] != 'TMT'))",
89 89
90 90 
           # features
91 91
... ... 
@@ -242,11 +242,11 @@ qcUI <- function(id) {
242 242 
                           #                  tags$h4("Calculation in progress...")),
243 243 
                           #tags$div(id='download_buttons')
244 244 
                           tags$br(),
245 
-                          conditionalPanel(condition="input['loadpage-DDA_DIA'] !== 'PTM'",
245 
+                          conditionalPanel(condition="input['loadpage-BIO'] !== 'PTM'",
246 246 
                                            disabled(downloadButton(ns("prepr_csv"),"Download .csv of feature level data")),
247 247 
                                            disabled(downloadButton(ns("summ_csv"),"Download .csv of protein level data"))
248 248 
                           ),
249 
-                          conditionalPanel(condition="input['loadpage-DDA_DIA'] == 'PTM'",
249 
+                          conditionalPanel(condition="input['loadpage-BIO'] == 'PTM'",
250 250 
                                            disabled(downloadButton(ns("prepr_csv_ptm"),"Download .csv of PTM feature level data")),
251 251 
                                            disabled(downloadButton(ns("summ_csv_ptm"),"Download .csv of PTM level data")),
252 252 
                                            tags$br(),
R/module-statmodel-server.R
History View file @ ab7f81f
... ... 
@@ -20,9 +20,9 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu
20 20 
   # choices of groups for contrast matrix
21 21
22 22 
   choices = reactive({
23 
-    if (loadpage_input()$DDA_DIA == "PTM" & (loadpage_input()$PTMTMT == "Yes" | loadpage_input()$filetype=='phil')){
23 
+    if (loadpage_input()$BIO == "PTM" & ((loadpage_input()$BIO == "PTM" & loadpage_input()$DDA_DIA == "TMT") | loadpage_input()$filetype=='phil')){
24 24 
       levels(preprocess_data()$PTM$ProteinLevelData$Condition)
25 
-    } else if(loadpage_input()$DDA_DIA == "PTM" & loadpage_input()$PTMTMT == "No"){
25 
+    } else if(loadpage_input()$BIO == "PTM" & (loadpage_input()$BIO == "PTM" & loadpage_input()$DDA_DIA != "TMT")){
26 26 
       levels(preprocess_data()$PTM$ProteinLevelData$GROUP)
27 27 
     } else if(loadpage_input()$DDA_DIA=="TMT"){
28 28 
       levels(preprocess_data()$ProteinLevelData$Condition)
... ... 
@@ -39,7 +39,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu
39 39
40 40
41 41 
   observe({
42 
-    if(loadpage_input()$DDA_DIA == "TMT" | loadpage_input()$DDA_DIA == "PTM"){
42 
+    if(loadpage_input()$DDA_DIA == "TMT" | loadpage_input()$BIO == "PTM"){
43 43 
       hide("Design")
44 44 
     }
45 45 
     else{
... ... 
@@ -302,8 +302,8 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu
302 302 
                    remove_norm_channel = TRUE,
303 303 
                    remove_empty_channel = TRUE
304 304 
                    )\n", sep = "")
305 
-    } else if (loadpage_input()$DDA_DIA == "PTM"){
306 
-      if (loadpage_input()$PTMTMT == "Yes" | loadpage_input()$filetype=='phil'){
305 
+    } else if (loadpage_input()$BIO == "PTM"){
306 
+      if ((loadpage_input()$BIO == "PTM" & loadpage_input()$DDA_DIA == "TMT") | loadpage_input()$filetype=='phil'){
307 307 
         dt = "TMT"
308 308 
       } else {
309 309 
         dt = "LabelFree"
... ... 
@@ -318,7 +318,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu
318 318 
       codes = paste(codes, "\n# Model-based comparison\n", sep = "")
319 319 
       codes = paste(codes,"model = MSstats::groupComparison(contrast.matrix, summarized)\n", sep = "")
320 320 
     }
321 
-    if (loadpage_input()$DDA_DIA == "PTM"){
321 
+    if (loadpage_input()$BIO == "PTM"){
322 322 
       codes = paste(codes, "groupComparisonPlotsPTM(data=model,
323 323 
                            type=\"Enter VolcanoPlot, Heatmap, or ComparisonPlot\",
324 324 
                            which.Comparison=\"all\",
... ... 
@@ -345,14 +345,15 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu
345 345 
   }
346 346
347 347 
   SignificantProteins = eventReactive(input$calculate,{
348 
-    if (loadpage_input()$DDA_DIA == "PTM"){
348 
+    if (loadpage_input()$BIO == "PTM"){
349 
+
349 350 
       data_comp = data_comparison()
350 351 
       sig_unadj = data_comp$PTM.Model[
351 
-        data_comp$PTM.Model$adj.pvalue < input$signif]
352 
+        data_comp$PTM.Model$adj.pvalue < input$signif,]
352 353 
       sig_prot = data_comp$PROTEIN.Model[
353 
-        data_comp$PROTEIN.Model$adj.pvalue < input$signif]
354 
+        data_comp$PROTEIN.Model$adj.pvalue < input$signif,]
354 355 
       sig_adj = data_comp$ADJUSTED.Model[
355 
-        data_comp$ADJUSTED.Model$adj.pvalue < input$signif]
356 
+        data_comp$ADJUSTED.Model$adj.pvalue < input$signif,]
356 357 
       significant = list(PTM.Model=sig_unadj,
357 358 
                          PROTEIN.Model=sig_prot,
358 359 
                          ADJUSTED.Model=sig_adj)
... ... 
@@ -387,7 +388,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu
387 388 
       return(path1_id)
388 389 
     }
389 390
390 
-    if (loadpage_input()$DDA_DIA=="PTM"){
391 
+    if (loadpage_input()$BIO=="PTM"){
391 392 
       plot1 = groupComparisonPlotsPTM(data_comparison(),
392 393 
                                       input$typeplot,
393 394 
                                       sig=input$sig,
R/module-statmodel-ui.R
History View file @ ab7f81f
... ... 
@@ -76,7 +76,7 @@ statmodelUI <- function(id) {
76 76 
           p("Please add a comparison matrix before modeling."),
77 77 
           disabled(actionButton(ns("calculate"), "Start")),
78 78 
           tags$hr(),
79 
-          conditionalPanel(condition = "input['loadpage-DDA_DIA'] == 'TMT' || (input['loadpage-PTMTMT'] == 'Yes')",
79 
+          conditionalPanel(condition = "input['loadpage-DDA_DIA'] == 'TMT' || (input['loadpage-BIO'] == 'PTM' && input['loadpage-DDA_DIA'] == 'TMT')",
80 80 
                            radioButtons(ns("moderated"),
81 81 
                                         label= h4("Empirical Bayes moderation",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
82 82 
                                                   div("TRUE will moderate t statistic; FALSE (default) uses ordinary t statistic.", class = "icon-tooltip")),
... ... 
@@ -154,7 +154,7 @@ statmodelUI <- function(id) {
154 154 
                           Volcano Plot comparison, you must save the results \
155 155 
                           as a pdf."),
156 156 
                  conditionalPanel(
157 
-                   condition = "input['loadpage-DDA_DIA'] !== 'PTM'",
157 
+                   condition = "input['loadpage-BIO'] !== 'PTM'",
158 158 
                    actionButton(ns("viewresults"),
159 159 
                                 "View plot in browser (only for one \
160 160 
                                      comparison/protein)")),
... ... 
@@ -172,7 +172,7 @@ statmodelUI <- function(id) {
172 172 
                                tags$br(),
173 173 
                         )),
174 174 
                uiOutput(ns("matrix")),
175 
-               conditionalPanel(condition = "input['loadpage-DDA_DIA']=='PTM'",
175 
+               conditionalPanel(condition = "input['loadpage-BIO']=='PTM'",
176 176 
                                 tabsetPanel(
177 177 
                                   tabPanel("Adjusted PTM Results",
178 178 
                                            uiOutput(ns("adj_table_results"))),
... ... 
@@ -182,7 +182,7 @@ statmodelUI <- function(id) {
182 182 
                                            uiOutput(ns("prot_table_results")))
183 183 
                                 )
184 184 
                ),
185 
-               conditionalPanel(condition = "input['loadpage-DDA_DIA']!=='PTM'",
185 
+               conditionalPanel(condition = "input['loadpage-BIO']!=='PTM'",
186 186 
                                 uiOutput(ns("table_results"))
187 187 
                ),
188 188 
                tags$br(),
R/server.R
History View file @ ab7f81f
... ... 
@@ -40,12 +40,12 @@ server <- function(input, output, session) {
40 40 
   # output$statmodel = renderUI(statmodel())
41 41 
   #
42 42 
   observe({
43 
-    if(input$"loadpage-DDA_DIA" %in% c("TMT", "PTM")){
43 
+    if(input$"loadpage-DDA_DIA" %in% c("TMT") && input$"loadpage-BIO" %in% c("PTM") ){
44 44 
       hideTab(inputId = "tablist", target = "PQ")
45 45 
       hideTab(inputId = "tablist", target = "Future")
46 46 
     }
47 47
48 
-    if(!(input$"loadpage-DDA_DIA" %in% c("TMT", "PTM"))){
48 
+    if(!(input$"loadpage-DDA_DIA" %in% c("TMT")) && !(input$"loadpage-BIO" %in% c("PTM"))){
49 49 
       showTab(inputId = "tablist", target = "PQ")
50 50 
       showTab(inputId = "tablist", target = "Future")
51 51 
     }
R/utils.R
History View file @ ab7f81f
... ... 
@@ -156,6 +156,7 @@ getAnnot2 <- function(input) {
156 156 
 }
157 157
158 158 
 getAnnot <- function(input) {
159 
+  print("Inside Annot");
159 160 
   annot = input$annot
160 161 
   if(is.null(annot)) {
161 162 
     return(NULL)
... ... 
@@ -211,33 +212,33 @@ getData <- function(input) {
211 212 
     return(NULL)
212 213 
   }
213 214 
   if(input$filetype == 'sample') {
214 
-    if(input$DDA_DIA == "SRM_PRM") {
215 
+    if(input$BIO != "PTM" && input$DDA_DIA =='LType' && input$LabelFreeType == "SRM_PRM") {
215 216 
       mydata = MSstats::DDARawData
216 217 
     }
217 
-    else if(input$DDA_DIA == "DDA") {
218 
+    else if(input$BIO != "PTM" &&  input$DDA_DIA == 'LType' && input$LabelFreeType == "DDA") {
218 219 
       mydata = MSstats::DDARawData
219 220 
     }
220 
-    else if(input$DDA_DIA == "DIA"){
221 
+    else if(input$BIO != "PTM" && input$DDA_DIA =='LType' && input$LabelFreeType == "DIA"){
221 222 
       mydata = read.csv(system.file("extdata/dataset.csv",
222 223 
                                     package = "MSstatsShiny"),
223 224 
                         header = TRUE, sep = ";")
224 225 
     }
225 
-    else if(input$DDA_DIA == "TMT"){
226 
+    else if(input$BIO != "PTM" && input$DDA_DIA == "TMT"){
226 227 
       mydata = PDtoMSstatsTMTFormat(input = MSstatsTMT::raw.pd,
227 228 
                                     annotation = MSstatsTMT::annotation.pd,
228 229 
                                     which.proteinid = input$which.proteinid,
229 230 
                                     use_log_file = FALSE
230 231 
       )
231 232 
     }
232 
-    else if (input$DDA_DIA == "PTM"){
233 
-      if (input$PTMTMT == "No"){
233 
+    else if (input$BIO == "PTM"){
234 
+      if (input$DDA_DIA != "TMT"){
234 235 
         mydata = MSstatsPTM::raw.input
235 236 
       } else {
236 237 
         mydata = MSstatsPTM::raw.input.tmt
237 238 
       }
238 239 
     }
239 240 
   }
240 
-  else if (input$DDA_DIA %in% c("PTM", "PTM_TMT")){
241 
+  else if (input$BIO == 'PTM' || (input$BIO == 'PTM' && input$DDA_DIA == 'TMT')){
241 242 
     if (input$filetype == 'maxq') {
242 243 
       mydata = read.csv(input$ptm_input$datapath,sep="\t")
243 244 
       print(input$globaldata$datapath)
... ... 
@@ -251,7 +252,7 @@ getData <- function(input) {
251 252
252 253 
       pg_maxq_ptm = try(read.csv(input$ptm_pgroup$datapath, sep="\t"),silent=TRUE)
253 254 
       annotation = try(read.csv(input$ptm_annot$datapath),silent=TRUE)
254 
-      if (input$PTMTMT_maxq_pd == "Yes"){
255 
+      if (input$BIO == "PTM" && input$DDA_DIA == "TMT"){
255 256 
         label = "TMT"
256 257 
       } else {
257 258 
         label = "LF"
... ... 
@@ -304,7 +305,7 @@ getData <- function(input) {
304 305 
         use_unmod_peptides=FALSE
305 306 
       }
306 307
307 
-      if (input$PTMTMT_maxq_pd == "Yes"){
308 
+      if (input$BIO == "PTM" && input$DDA_DIA == "TMT"){
308 309 
         label = "TMT"
309 310 
       } else {
310 311 
         label = "LF"
... ... 
@@ -377,7 +378,7 @@ getData <- function(input) {
377 378 
     if(input$filetype=='spec' || input$filetype=='spmin'){
378 379 
       infile = input$data1
379 380 
     }
380 
-    else if(input$filetype=='phil' & input$DDA_DIA != "PTM"){
381 
+    else if(input$filetype=='phil' & input$BIO != "PTM"){
381 382 
       mydata = read.csv(input$data$datapath)
382 383
383 384 
     }
... ... 
@@ -416,28 +417,6 @@ getData <- function(input) {
416 417 
       data = read.csv(input$skylinedata$datapath, header = TRUE, sep = input$sep,
417 418 
                       stringsAsFactors=FALSE)
418 419 
       # }
419 
-      if(input$DDA_DIA=="DDA" ){
420 
-        data = data[which(data$Fragment.Ion %in% c("precursor",
421 
-                                                   "precursor [M+1]",
422 
-                                                   "precursor [M+2]")),]
423 
-
424 
-        mydata = SkylinetoMSstatsFormat(data,
425 
-                                        annotation = getAnnot(input),
426 
-                                        fewMeasurements="remove",
427 
-                                        removeProtein_with1Feature = input$remove,
428 
-                                        use_log_file = FALSE)
429 
-      }
430 
-      else if(input$DDA_DIA=="DIA"){
431 
-        mydata = SkylinetoMSstatsFormat(data,
432 
-                                        annotation = getAnnot(input),
433 
-                                        filter_with_Qvalue = TRUE,
434 
-                                        qvalue_cutoff = 0.01,
435 
-                                        fewMeasurements="remove",
436 
-                                        removeProtein_with1Feature = TRUE,
437 
-                                        use_log_file = FALSE)
438 
-
439 
-      }
440 
-      else if(input$DDA_DIA=="SRM_PRM") {
441 420 
         mydata = SkylinetoMSstatsFormat(data,
442 421 
                                         annotation = getAnnot(input),
443 422 
                                         filter_with_Qvalue = TRUE,
... ... 
@@ -445,8 +424,6 @@ getData <- function(input) {
445 424 
                                         fewMeasurements="remove",
446 425 
                                         removeProtein_with1Feature = TRUE,
447 426 
                                         use_log_file = FALSE)
448 
-      }
449 
-
450 427 
     }
451 428 
     else if(input$filetype == 'maxq') {
452 429 
       cat(file=stderr(), "Reached in maxq\n")
... ... 
@@ -546,6 +523,8 @@ getData <- function(input) {
546 523 
                                           qvalue_cutoff = 0.01, ## same as default
547 524 
                                           removeProtein_with1Feature = TRUE,
548 525 
                                           use_log_file = FALSE)
526 
+      print("Mydata from mstats")
527 
+      print(mydata)
549 528 
     }
550 529 
     else if(input$filetype == 'open') {
551 530
... ... 
@@ -628,11 +607,12 @@ getData <- function(input) {
628 607 
   }
629 608
630 609
631 
-  if (input$level == "Peptide"){
610 
+  if (input$BIO == "Peptide"){
632 611 
     mydata$ProteinName = mydata$PeptideSequence
633 612 
   }
634 613
635 614 
   remove_modal_spinner()
615 
+
636 616 
   return(mydata)
637 617 
 }
638 618
... ... 
@@ -647,30 +627,30 @@ library(MSstatsPTM)\n", sep = "")
647 627 
                 "\n# MSstatsPTM version ", packageVersion("MSstatsPTM"), sep = "")
648 628 
   codes = paste(codes, "\n\n# Read data\n", sep = "")
649 629 
   if(input$filetype == 'sample') {
650 
-    if(input$DDA_DIA == "SRM_PRM") {
630 
+    if(input$BIO != "PTM" &&  input$DDA_DIA =='LType' && input$LabelFreeType == "SRM_PRM") {
651 631 
       codes = paste(codes, "data = SRM_yeast\n", sep = "")
652 632 
     }
653 
-    else if(input$DDA_DIA == "DDA") {
633 
+    else if(input$BIO != "PTM" &&  input$DDA_DIA =='LType' && input$LabelFreeType == "DDA") {
654 634 
       codes = paste(codes, "data = DDARawData\n", sep = "")
655 635 
     }
656 
-    else if(input$DDA_DIA == "DIA"){
636 
+    else if(input$BIO != "PTM" &&  input$DDA_DIA =='LType' && input$LabelFreeType == "DIA"){
657 637 
       codes = paste(codes, "data = read.csv(\"dataset.csv\", header = TRUE, sep = \";\")\n", sep = "")
658 638 
     }
659 
-    else if(input$DDA_DIA == "TMT"){
639 
+    else if(input$BIO != "PTM" &&  input$DDA_DIA == "TMT"){
660 640 
       codes = paste(codes, "data = PDtoMSstatsTMTFormat(input = MSstatsTMT::raw.pd,
661 641 
                                        annotation = MSstatsTMT::annotation.pd,
662 642 
                                        which.proteinid =\'", input$which.proteinid,"\',\n\t\t\t\t       ",
663 643 
                     "use_log_file = FALSE)\n", sep = "")
664 
-    } else if (input$DDA_DIA == "PTM") {
665 
-      if (input$PTMTMT == "Yes"){
644 
+    } else if (input$BIO == "PTM") {
645 
+      if (input$BIO == "PTM" && input$DDA_DIA == "TMT"){
666 646 
         codes = paste(codes, "data = MSstatsPTM::raw.input.tmt\n", sep = "")
667 
-      } else if (input$PTMTMT == "No"){
647 
+      } else if (input$BIO == "PTM" && input$DDA_DIA != "TMT"){
668 648 
         codes = paste(codes, "data = MSstatsPTM::raw.input\n", sep = "")
669 649 
       }
670 650 
     }
671 651
672 652 
   } else if (input$filetype == "msstats") {
673 
-    if (input$DDA_DIA == "PTM") {
653 
+    if (input$BIO == "PTM") {
674 654 
       codes = paste(codes, "\nptm_data = read.csv(\'Enter PTM data file path here\')\nglobal_data = read.csv(\'Enter unmod data file path here\')\ndata = list(PTM = ptm_data, PROTEIN = unmod)\n")
675 655 
     } else {
676 656 
       codes = paste(codes, "data = read.csv(\'Enter MSstats formatted data file path here\')\n")
... ... 
@@ -716,7 +696,7 @@ library(MSstatsPTM)\n", sep = "")
716 696 
                                          annotation=an_maxq,
717 697 
                                          proteinGroups=\'", input$which.proteinid,"\',\n\t\t\t\t       ",
718 698 
                       "use_log_file = FALSE)\n", sep = "")
719 
-      } else if (input$DDA_DIA=="PTM"){
699 
+      } else if (input$BIO=="PTM"){
720 700 
         codes = paste(codes, "sites.data = read.csv(\"insert your PTM site data filepath\")\n data = MaxQtoMSstatsPTMFormat(sites.data, an_maxq, ev_maxq, pg_maxq, an_maxq)\n",
721 701 
                       sep="")
722 702 
       } else {
... ... 
@@ -829,7 +809,7 @@ library(MSstatsPTM)\n", sep = "")
829 809
830 810 
       codes = paste(codes, "data = PhilosophertoMSstatsTMTFormat(data,
831 811 
                                        annotation = annot_file)\n", sep = "")
832 
-    }else if (input$filetype == 'phil' & input$DDA_DIA == "PTM"){
812 
+    }else if (input$filetype == 'phil' & input$BIO == "PTM"){
833 813 
       codes = paste(codes,"data = read.csv(\"insert your msstats filepath\")\n"
834 814 
                     , sep = "")
835 815 
       codes = paste(codes,"annot_file = read.csv(\"insert your annotation filepath\")\n"
... ... 
@@ -851,7 +831,7 @@ library(MSstatsPTM)\n", sep = "")
851 831 
     }
852 832 
   }
853 833
854 
-  if (input$DDA_DIA != "PTM"){
834 
+  if (input$BIO != "PTM"){
855 835 
     codes = paste(codes,"data = unique(as.data.frame(data))\n", sep = "")
856 836 
   }
857 837 
   return(codes)
... ... 
@@ -862,13 +842,13 @@ getSummary1 <- function(input, df,annot_df) {
862 842 
   # df = getData(input)
863 843 
   print("+++++++++ In getSummary1 +++++++++")
864 844 
   # annot_df = getAnnot(input)
865 
-  if (input$DDA_DIA != "PTM"){
845 
+  if (input$BIO != "PTM"){
866 846 
     df = as.data.frame(df)
867 847 
     df = df %>% filter(!Condition %in% c("Norm", "Empty"))
868 848 
     nf = ifelse("Fraction" %in% colnames(df),n_distinct(df$Fraction),1)
869 849 
   }
870 850
871 
-  if(input$DDA_DIA=="TMT"){
851 
+  if(input$BIO != "PTM" && input$DDA_DIA=="TMT"){
872 852 
     if(is.null(annot_df)){
873 853 
       df1 = df %>% summarise("Number of Conditions" = n_distinct(Condition),
874 854 
                              "Number of Biological Replicates" = n_distinct(BioReplicate),
... ... 
@@ -886,10 +866,10 @@ getSummary1 <- function(input, df,annot_df) {
886 866 
                                    "Number of Technical Replicates" = n_distinct(TechRepMixture))
887 867 
     }
888 868
889 
-  } else if (input$DDA_DIA == "PTM"){
869 
+  } else if (input$BIO == "PTM"){
890 870 
     ptm_df = as.data.frame(df$PTM)
891 871 
     unmod_df = as.data.frame(df$PROTEIN)
892 
-    if (input$PTMTMT == "Yes" | input$filetype=='phil'){
872 
+    if ((input$BIO == "PTM" & input$DDA_DIA == "TMT") | input$filetype=='phil'){
893 873
894 874 
       ptm_df1 = ptm_df %>% summarise("Number of Conditions" = n_distinct(Condition),
895 875 
                                      "Number of PTM Mixtures" = n_distinct(Mixture),
... ... 
@@ -921,7 +901,7 @@ getSummary1 <- function(input, df,annot_df) {
921 901 
     )
922 902 
   }
923 903
924 
-  if (input$DDA_DIA != "PTM"){
904 
+  if (input$BIO != "PTM"){
925 905 
     df2 = df %>% group_by(Condition, Run) %>% summarise("Condition_Run" = n()) %>% ungroup() %>%
926 906 
       select("Condition_Run")
927 907 
     df3 = df %>% group_by(Run, BioReplicate) %>% summarise("BioReplicate_Run" = n()) %>% ungroup() %>%
... ... 
@@ -956,18 +936,18 @@ getSummary1 <- function(input, df,annot_df) {
956 936 
 getSummary2 <- function(input,df) {
957 937 
   # df = getData(input)
958 938 
   print("+++++++++ In getSummary2 +++++++++")
959 
-  print(input$PTMTMT)
960 
-  if(input$DDA_DIA=="TMT"){
939 
+  #print(input$PTMTMT)
940 
+  if(input$BIO != "PTM" && input$DDA_DIA=="TMT"){
961 941 
     df = as.data.frame(df)
962 942 
     df = df %>% mutate("FEATURES" = paste(ProteinName, PeptideSequence, Charge,
963 943 
                                           sep = '_'))
964 
-  } else if (input$DDA_DIA == "PTM" & (input$PTMTMT == "Yes" | input$filetype=='phil')){
944 
+  } else if (input$BIO == "PTM" & ((input$BIO == "PTM" & input$DDA_DIA == "TMT" )| input$filetype=='phil')){
965 945 
     df_ptm = as.data.frame(df$PTM) %>% mutate("FEATURES" = paste(ProteinName, PeptideSequence,
966 946 
                                                                  Charge, sep = '_'))
967 947 
     df_prot = as.data.frame(df$PROTEIN) %>% mutate("FEATURES" = paste(ProteinName,
968 948 
                                                                       PeptideSequence,
969 949 
                                                                       Charge, sep = '_'))
970 
-  } else if (input$DDA_DIA == "PTM" & input$PTMTMT == "No"){
950 
+  } else if (input$BIO == "PTM" & (input$BIO == "PTM" & input$DDA_DIA != "TMT" )){
971 951 
     df_ptm = as.data.frame(df$PTM) %>% mutate("FEATURES" = paste(PeptideSequence,
972 952 
                                                                  PrecursorCharge,
973 953 
                                                                  FragmentIon,
... ... 
@@ -984,7 +964,7 @@ getSummary2 <- function(input,df) {
984 964 
                                           sep = '_'))
985 965 
   }
986 966
987 
-  if (input$DDA_DIA != "PTM"){
967 
+  if (input$BIO != "PTM"){
988 968
989 969 
     df1 = df %>% summarise("Number of Proteins" = n_distinct(ProteinName),
990 970 
                            "Number of Peptides" = n_distinct(PeptideSequence),
... ... 
@@ -1064,13 +1044,13 @@ preprocessData <- function(qc_input,loadpage_input,input_data ) {
1064 1044 
   MSstatsLogsSettings(FALSE)
1065 1045 
   ## Here we run the underlying functions for MSstats and MSstatsTMT
1066 1046 
   ## summarization. Done so we can loop over proteins and create a progress bar
1067 
-  if(loadpage_input$DDA_DIA == "PTM" & (loadpage_input$PTMTMT == "Yes" | loadpage_input$filetype=='phil')){
1047 
+  if(loadpage_input$BIO == "PTM" & ((loadpage_input$BIO == "PTM" & loadpage_input$DDA_DIA == "TMT" ) | loadpage_input$filetype=='phil')){
1068 1048
1069 1049 
     preprocessed_ptm = MSstatsShiny::tmt_summarization_loop(input_data$PTM, qc_input,loadpage_input)
1070 1050 
     preprocessed_unmod = MSstatsShiny::tmt_summarization_loop(input_data$PROTEIN, qc_input,loadpage_input)
1071 1051 
     preprocessed = list(PTM = preprocessed_ptm, PROTEIN = preprocessed_unmod)
1072 1052
1073 
-  } else if (loadpage_input$DDA_DIA == "PTM" & loadpage_input$PTMTMT == "No"){
1053 
+  } else if (loadpage_input$BIO == "PTM" & (loadpage_input$BIO == "PTM" & loadpage_input$DDA_DIA != "TMT" )){
1074 1054
1075 1055 
     preprocessed_ptm = MSstatsShiny::lf_summarization_loop(input_data$PTM, qc_input, loadpage_input)
1076 1056 
     preprocessed_unmod = MSstatsShiny::lf_summarization_loop(input_data$PROTEIN, qc_input, loadpage_input)
... ... 
@@ -1113,8 +1093,8 @@ preprocessDataCode <- function(qc_input,loadpage_input) {
1113 1093 
                             originalPlot = TRUE,
1114 1094 
                             summaryPlot =", qc_input$summ,",\t\t\t\t
1115 1095 
                             address = FALSE)\n", sep="")
1116 
-  } else if (loadpage_input$DDA_DIA == "PTM"){
1117 
-    if (loadpage_input$PTMTMT == "Yes" | loadpage_input$filetype=='phil'){
1096 
+  } else if (loadpage_input$BIO == "PTM"){
1097 
+    if ((loadpage_input$BIO == "PTM" & loadpage_input$DDA_DIA == "TMT" ) | loadpage_input$filetype=='phil'){
1118 1098 
       codes = paste(codes, "\n# use MSstats for protein summarization\n", sep = "")
1119 1099 
       codes = paste(codes, "summarized = MSstatsPTM::dataSummarizationPTM_TMT(data,
1120 1100 
                      method = '",qc_input$summarization,"\',\t\t\t\t
... ... 
@@ -1190,7 +1170,7 @@ dataComparison <- function(statmodel_input,qc_input,loadpage_input,matrix,input_
1190 1170 
   print("+++++++++ In Data Comparison +++++++++")
1191 1171 
   # input_data = preprocessData(qc_input,loadpage_input,get_data())
1192 1172 
   contrast.matrix = matrix
1193 
-  if (loadpage_input$DDA_DIA == "PTM" & (loadpage_input$PTMTMT == "Yes" | loadpage_input$filetype=='phil')){
1173 
+  if (loadpage_input$BIO == "PTM" & ((loadpage_input$BIO == "PTM" & loadpage_input$DDA_DIA == "TMT" ) | loadpage_input$filetype=='phil')){
1194 1174 
     model_ptm = MSstatsShiny::tmt_model(input_data$PTM, statmodel_input, contrast.matrix)
1195 1175 
     model_protein = MSstatsShiny::tmt_model(input_data$PROTEIN, statmodel_input, contrast.matrix)
1196 1176 
     model_adj = MSstatsShiny::apply_adj(model_ptm$ComparisonResult,
... ... 
@@ -1199,7 +1179,7 @@ dataComparison <- function(statmodel_input,qc_input,loadpage_input,matrix,input_
1199 1179 
                  'PROTEIN.Model' = model_protein$ComparisonResult,
1200 1180 
                  'ADJUSTED.Model' = model_adj)
1201 1181
1202 
-  } else if(loadpage_input$DDA_DIA == "PTM" & loadpage_input$PTMTMT == "No"){
1182 
+  } else if(loadpage_input$BIO == "PTM" & (loadpage_input$BIO == "PTM" & loadpage_input$DDA_DIA != "TMT" )){
1203 1183 
     model_ptm = MSstatsShiny::lf_model(input_data$PTM, contrast.matrix)
1204 1184 
     model_protein = MSstatsShiny::lf_model(input_data$PROTEIN, contrast.matrix)
1205 1185 
     model_adj = MSstatsShiny::apply_adj(model_ptm$ComparisonResult,
README.md
History View file @ ab7f81f
... ... 
@@ -16,13 +16,16 @@ we recommend processing large datasets using a local installation.
16 16
17 17 
 ### Bioconductor
18 18
19 
-For large file processing, it is recommend you use a local install of the application. The easiest way to install the application locally is via [Bioconductor](https://bioconductor.org/packages/release/bioc/html/MSstatsShiny.html)
19 
+To install the application via Bioconductor, please use the following steps.
20 
+
21 
+1. Download [R](https://www.r-project.org/) and [RStudio](https://www.rstudio.com/products/rstudio/download/) - [How to](https://rstudio-education.github.io/hopr/starting.html). **Note R version must be >= 4.3**
22 
+2. Intall the package via [Bioconductor](https://bioconductor.org/packages/release/bioc/html/MSstatsShiny.html)
20 23
21 24 
 ### Github
22 25
23 26 
 To install the application via Github, please use the following steps.
24 27
25 
-1. Download [R](https://www.r-project.org/) and [RStudio](https://www.rstudio.com/products/rstudio/download/) - [How to](https://rstudio-education.github.io/hopr/starting.html). **Note R version must be >= 4.2**
28 
+1. Download [R](https://www.r-project.org/) and [RStudio](https://www.rstudio.com/products/rstudio/download/) - [How to](https://rstudio-education.github.io/hopr/starting.html). **Note R version must be >= 4.3**
26 29 
 2. Install the package by executing `devtools::install_github("Vitek-Lab/MSstatsShiny")` in the console.
27 30 
 3. Run the application by executing `library(MSstatsShiny)` and `launch_MSstatsShiny()` or `MSstatsShiny::launch_MSstatsShiny()` in the console.
28 31
tests/testthat/test-utils.R
History View file @ ab7f81f
... ... 
@@ -345,7 +345,7 @@ test_that("getAnnot2 returns an error message when given invalid input", {
345 345 
 test_that("getAnnot returns a data frame when given valid input", {
346 346 
   suppressWarnings({
347 347 
     mock_input$filetype = "sample"
348 
-    mock_input$DDA_DIA = "DIA"
348 
+    mock_input$DDA_DIA = "LType"
349 349 
     mock_input$annot$datapath = test_file_tsv
350 350 
     annot <- getAnnot(mock_input)
351 351 
     expect_s3_class(annot, "data.frame")
... ... 
@@ -355,7 +355,7 @@ test_that("getAnnot returns a data frame when given valid input", {
355 355 
 test_that("getAnnot returns NULL when given a null input", {
356 356 
   suppressWarnings({
357 357 
     mock_input$filetype = "sample"
358 
-    mock_input$DDA_DIA = "DIA"
358 
+    mock_input$DDA_DIA = "LType"
359 359 
     mock_input$annot <- NULL
360 360 
     annot <- getAnnot(mock_input)
361 361 
     expect_equal(annot, NULL)
... ... 
@@ -365,7 +365,7 @@ test_that("getAnnot returns NULL when given a null input", {
365 365 
 test_that("getAnnot returns an error message when given invalid input", {
366 366 
   suppressWarnings({
367 367 
     mock_input$filetype = "sample"
368 
-    mock_input$DDA_DIA = "DIA"
368 
+    mock_input$DDA_DIA = "LType"
369 369 
     mock_input$annot$datapath <- '/path/to'
370 370 
     annot <- getAnnot(mock_input)
371 371 
     expect_equal(annot, "File load error. Please ensure file is in csv format.")
... ... 
@@ -411,19 +411,24 @@ test_that("Empty file type returns NULL", {
411 411
412 412 
 test_that("sample file type returns expected value", {
413 413 
   mock_input$filetype = "sample"
414 
-  ips_vec <- c("SRM_PRM", "DIA", "DDA")
414 
+  mock_input$BIO <- "Protein"
415 
+  mock_input$DDA_DIA <- "LType"
416 
+  ips_vec <- c("SRM_PRM" , "DDA" ,
417 
+               "DIA")
415 418 
   for (ddadia in ips_vec) {
416 
-    mock_input$DDA_DIA <- ddadia
419 
+    mock_input$LabelFreeType <- ddadia
417 420 
     output <- getData(mock_input)
418 
-    expect_is(output, "data.frame")
421 
+    expect_type(output, "list")
419 422 
   }
420 423
421 
-  mock_input$DDA_DIA <- "PTM"
424 
+  mock_input$DDA_DIA <- "LType"
425 
+  mock_input$BIO <- "PTM"
422 426 
   output <- getData(mock_input)
423 427 
   print(typeof(output))
424 428 
   expect_type(output,"list")
425 429
426 
-  mock_input$PTMTMT <- "Yes"
430 
+  mock_input$DDA_DIA <- "TMT"
431 
+  mock_input$BIO <- "PTM"
427 432 
   output <- getData(mock_input)
428 433 
   print(typeof(output))
429 434 
   expect_type(output,"list")
... ... 
@@ -431,7 +436,9 @@ test_that("sample file type returns expected value", {
431 436
432 437 
 test_that("dda maxquant", {
433 438 
   suppressWarnings({
434 
-    mock_input$DDA_DIA <- "DDA"
439 
+    mock_input$BIO <- "Protein"
440 
+
441 
+    mock_input$DDA_DIA <- "LType"
435 442 
     mock_input$filetype = "maxq"
436 443
437 444 
     stub(getData,"getEvidence",data.table::fread(system.file("tinytest/raw_data/MaxQuant/mq_ev.csv",
... ... 
@@ -451,7 +458,8 @@ test_that("dda maxquant", {
451 458
452 459 
 test_that("dda pd", {
453 460 
   suppressWarnings({
454 
-    mock_input$DDA_DIA <- "DDA"
461 
+    mock_input$BIO <- "Protein"
462 
+    mock_input$DDA_DIA <- "LType"
455 463 
     mock_input$filetype = "PD"
456 464 
     mock_input$sep = ","
457 465
... ... 
@@ -469,7 +477,8 @@ test_that("dda pd", {
469 477
470 478 
 test_that("dda prog", {
471 479 
   suppressWarnings({
472 
-    mock_input$DDA_DIA <- "DDA"
480 
+    mock_input$BIO <- "Protein"
481 
+    mock_input$DDA_DIA <- "LType"
473 482 
     mock_input$filetype = "prog"
474 483 
     mock_input$sep = ","
475 484
... ... 
@@ -488,7 +497,8 @@ test_that("dda prog", {
488 497
489 498 
 test_that("dda dia skyline", {
490 499 
   suppressWarnings({
491 
-    mock_input$DDA_DIA <- "DDA"
500 
+    mock_input$BIO <- "Protein"
501 
+    mock_input$DDA_DIA <- "LType"
492 502 
     mock_input$filetype = "sky"
493 503 
     mock_input$sep = ","
494 504
... ... 
@@ -502,7 +512,7 @@ test_that("dda dia skyline", {
502 512 
     expect_type(output,"list")
503 513 
     expect_identical(names(output), expected_names)
504 514
505 
-    mock_input$DDA_DIA <- "DIA"
515 
+    mock_input$DDA_DIA <- "LType"
506 516 
     output <- getData(mock_input)
507 517 
     expected_names <- c("ProteinName","PeptideSequence","PrecursorCharge","FragmentIon","ProductCharge","IsotopeLabelType","Condition","BioReplicate","Run","Fraction","Intensity")
508 518 
     expect_type(output,"list")
... ... 
@@ -512,7 +522,8 @@ test_that("dda dia skyline", {
512 522
513 523 
 test_that("dda openms", {
514 524 
   suppressWarnings({
515 
-    mock_input$DDA_DIA <- "DDA"
525 
+    mock_input$BIO <- "Protein"
526 
+    mock_input$DDA_DIA <- "LType"
516 527 
     mock_input$filetype = "openms"
517 528 
     mock_input$sep = ","
518 529
... ... 
@@ -528,7 +539,8 @@ test_that("dda openms", {
528 539
529 540 
 test_that("dia diaumpire", {
530 541 
   suppressWarnings({
531 
-    mock_input$DDA_DIA <- "DIA"
542 
+    mock_input$BIO <- "Protein"
543 
+    mock_input$DDA_DIA <- "LType"
532 544 
     mock_input$filetype = "ump"
533 545
534 546 
     stub(getData,"getFragSummary",data.table::fread(system.file("tinytest/raw_data/DIAUmpire/dia_frag.csv",
... ... 
@@ -549,7 +561,8 @@ test_that("dia diaumpire", {
549 561
550 562 
 test_that("dia spectronaut", {
551 563 
   suppressWarnings({
552 
-    mock_input$DDA_DIA <- "DIA"
564 
+    mock_input$BIO <- "Protein"
565 
+    mock_input$DDA_DIA <- "LType"
553 566 
     mock_input$filetype = "spec"
554 567
555 568 
     stub(getData,"getAnnot",NULL)
... ... 
@@ -565,7 +578,8 @@ test_that("dia spectronaut", {
565 578
566 579 
 test_that("dia openswath", {
567 580 
   suppressWarnings({
568 
-    mock_input$DDA_DIA <- "DIA"
581 
+    mock_input$BIO  <- "Protein"
582 
+    mock_input$DDA_DIA <- "LType"
569 583 
     mock_input$filetype = "open"
570 584 
     mock_input$sep = "\t"
571 585
... ... 
@@ -582,6 +596,7 @@ test_that("dia openswath", {
582 596
583 597 
 test_that("tmt maxquant", {
584 598 
   suppressWarnings({
599 
+    mock_input$BIO <- "Protein"
585 600 
     mock_input$DDA_DIA <- "TMT"
586 601 
     mock_input$filetype = "maxq"
587 602
... ... 
@@ -605,6 +620,7 @@ test_that("tmt maxquant", {
605 620
606 621 
 test_that("tmt openms", {
607 622 
   suppressWarnings({
623 
+    mock_input$BIO <- "Protein"
608 624 
     mock_input$DDA_DIA <- "TMT"
609 625 
     mock_input$filetype = "openms"
610 626 
     mock_input$sep = ","
... ... 
@@ -621,6 +637,7 @@ test_that("tmt openms", {
621 637
622 638 
 test_that("tmt spectromine", {
623 639 
   suppressWarnings({
640 
+    mock_input$BIO <-"Protein"
624 641 
     mock_input$DDA_DIA <- "TMT"
625 642 
     mock_input$filetype = "spmin"
626 643
... ... 
@@ -657,20 +674,26 @@ test_that("get data code filetype sample", {
657 674 
   suppressWarnings({
658 675 
     mock_input$filetype = "sample"
659 676
660 
-    mock_input$DDA_DIA <- "SRM_PRM"
677 
+    mock_input$BIO <- "Protein"
678 
+    mock_input$DDA_DIA <- "LType"
679 
+    mock_input$LabelFreeType ="SRM_PRM"
661 680 
     output <- getDataCode(mock_input)
662 681 
     expect_type(output,"character")
663 682
664 
-    mock_input$DDA_DIA <- "DDA"
683 
+    mock_input$BIO <- "Protein"
684 
+    mock_input$DDA_DIA <- "LType"
685 
+    mock_input$LabelFreeType ="DDA"
665 686 
     output <- getDataCode(mock_input)
666 687 
     expect_type(output,"character")
667 688
668 
-    mock_input$DDA_DIA <- "DIA"
689 
+    mock_input$BIO <- "Protein"
690 
+    mock_input$DDA_DIA <- "LType"
691 
+    mock_input$LabelFreeType ="DIA"
669 692 
     output <- getDataCode(mock_input)
670 693 
     expect_type(output,"character")
671 694
672 
-    mock_input$DDA_DIA <- "PTM"
673 
-    mock_input$PTMTMT <- "Yes"
695 
+    mock_input$BIO <- "Protein"
696 
+    mock_input$DDA_DIA <- "TMT"
674 697 
     output <- getDataCode(mock_input)
675 698 
     expect_type(output,"character")
676 699 
   })
... ... 
@@ -680,11 +703,11 @@ test_that("get data code filetype msstats", {
680 703 
   suppressWarnings({
681 704 
     mock_input$filetype = "msstats"
682 705
683 
-    mock_input$DDA_DIA <- "PTM"
706 
+    mock_input$BIO <- "PTM"
684 707 
     output <- getDataCode(mock_input)
685 708 
     expect_type(output,"character")
686 709
687 
-    mock_input$DDA_DIA <- "DDA"
710 
+    mock_input$BIO <- "Protein"
688 711 
     output <- getDataCode(mock_input)
689 712 
     expect_type(output,"character")
690 713 
   })
... ... 
@@ -692,9 +715,10 @@ test_that("get data code filetype msstats", {
692 715
693 716 
 test_that("get data code filetype 10col", {
694 717 
   suppressWarnings({
718 
+    mock_input$BIO <- "Protein"
695 719 
     mock_input$filetype = "10col"
696 720
697 
-    mock_input$DDA_DIA <- "DDA"
721 
+    mock_input$DDA_DIA <- "LType"
698 722 
     output <- getDataCode(mock_input)
699 723 
     expect_type(output,"character")
700 724 
   })
... ... 
@@ -702,13 +726,14 @@ test_that("get data code filetype 10col", {
702 726
703 727 
 test_that("get data code filetype sky", {
704 728 
   suppressWarnings({
729 
+    mock_input$BIO <- "Protein"
705 730 
     mock_input$filetype = "sky"
706 731
707 
-    mock_input$DDA_DIA <- "DDA"
732 
+    mock_input$DDA_DIA <- "LType"
708 733 
     output <- getDataCode(mock_input)
709 734 
     expect_type(output,"character")
710 735
711 
-    mock_input$DDA_DIA <- "DIA"
736 
+    mock_input$DDA_DIA <- "LType"
712 737 
     output <- getDataCode(mock_input)
713 738 
     expect_type(output,"character")
714 739 
   })
... ... 
@@ -717,16 +742,17 @@ test_that("get data code filetype sky", {
717 742 
 test_that("get data code filetype maxq", {
718 743 
   suppressWarnings({
719 744 
     mock_input$filetype = "maxq"
720 
-
745 
+    mock_input$BIO <- "Protein"
721 746 
     mock_input$DDA_DIA <- "TMT"
722 747 
     output <- getDataCode(mock_input)
723 748 
     expect_type(output,"character")
724 749
725 
-    mock_input$DDA_DIA <- "PTM"
750 
+    mock_input$BIO  <- "PTM"
726 751 
     output <- getDataCode(mock_input)
727 752 
     expect_type(output,"character")
728 753
729 
-    mock_input$DDA_DIA <- "DIA"
754 
+    mock_input$BIO <- "Protein"
755 
+    mock_input$DDA_DIA <- "LType"
730 756 
     output <- getDataCode(mock_input)
731 757 
     expect_type(output,"character")
732 758 
   })
... ... 
@@ -735,8 +761,8 @@ test_that("get data code filetype maxq", {
735 761 
 test_that("get data code filetype prog", {
736 762 
   suppressWarnings({
737 763 
     mock_input$filetype = "prog"
738 
-
739 
-    mock_input$DDA_DIA <- "DIA"
764 
+    mock_input$BIO <- "Protein"
765 
+    mock_input$DDA_DIA <- "LType"
740 766 
     output <- getDataCode(mock_input)
741 767 
     expect_type(output,"character")
742 768 
   })
... ... 
@@ -745,12 +771,13 @@ test_that("get data code filetype prog", {
745 771 
 test_that("get data code filetype PD", {
746 772 
   suppressWarnings({
747 773 
     mock_input$filetype = "PD"
748 
-
774 
+    mock_input$BIO <- "Protein"
749 775 
     mock_input$DDA_DIA <- "TMT"
750 776 
     output <- getDataCode(mock_input)
751 777 
     expect_type(output,"character")
752 778
753 
-    mock_input$DDA_DIA <- "DIA"
779 
+    mock_input$BIO <- "Protein"
780 
+    mock_input$DDA_DIA <- "LType"
754 781 
     output <- getDataCode(mock_input)
755 782 
     expect_type(output,"character")
756 783 
   })
... ... 
@@ -759,32 +786,32 @@ test_that("get data code filetype PD", {
759 786 
 test_that("get data code filetype spec & open & openms", {
760 787 
   suppressWarnings({
761 788 
     mock_input$filetype = "spec"
762 
-
763 
-    mock_input$DDA_DIA <- "DIA"
789 
+    mock_input$BIO <- "Protein"
790 
+    mock_input$DDA_DIA <- "LType"
764 791 
     output <- getDataCode(mock_input)
765 792 
     expect_type(output,"character")
766 793
767 794 
     mock_input$filetype = "open"
768 795
769 
-    mock_input$DDA_DIA <- "DIA"
796 
+    mock_input$DDA_DIA <- "LType"
770 797 
     output <- getDataCode(mock_input)
771 798 
     expect_type(output,"character")
772 799
773 800 
     mock_input$filetype = "openms"
774 801
775 
-    mock_input$DDA_DIA <- "DIA"
802 
+    mock_input$DDA_DIA <- "LType"
776 803 
     output <- getDataCode(mock_input)
777 804 
     expect_type(output,"character")
778 805
779 806 
     mock_input$filetype = "spim"
780 807
781 
-    mock_input$DDA_DIA <- "DIA"
808 
+    mock_input$DDA_DIA <- "LType"
782 809 
     output <- getDataCode(mock_input)
783 810 
     expect_type(output,"character")
784 811
785 812 
     mock_input$filetype = "phil"
786 813
787 
-    mock_input$DDA_DIA <- "DIA"
814 
+    mock_input$DDA_DIA <- "LType"
788 815 
     output <- getDataCode(mock_input)
789 816 
     expect_type(output,"character")
790 817 
   })
... ... 
@@ -816,8 +843,8 @@ mockGetData = function(mock_input) {
816 843 
 test_that("get summary 1 PTM PTMTMT:Yes", {
817 844 
   suppressWarnings({
818 845 
     mock_input$filetype = "sample"
819 
-    mock_input$DDA_DIA <- "PTM"
820 
-    mock_input$PTMTMT <- "Yes"
846 
+    mock_input$BIO <- "PTM"
847 
+    mock_input$DDA_DIA <- "TMT"
821 848 
     stub(getSummary1,"getData",mockGetData(mock_input))
822 849
823 850 
     output <- getSummary1(mock_input,getData(mock_input))
... ... 
@@ -831,8 +858,8 @@ test_that("get summary 1 PTM PTMTMT:Yes", {
831 858 
 test_that("get summary 1 PTM PTMTMT:No", {
832 859 
   suppressWarnings({
833 860 
     mock_input$filetype = "sample"
834 
-    mock_input$DDA_DIA <- "PTM"
835 
-    mock_input$PTMTMT <- "No"
861 
+    mock_input$BIO <- "PTM"
862 
+    mock_input$DDA_DIA <- "LType"
836 863 
     stub(getSummary1,"getData",mockGetData(mock_input))
837 864
838 865 
     output <- getSummary1(mock_input,getData(mock_input))
... ... 
@@ -845,8 +872,10 @@ test_that("get summary 1 PTM PTMTMT:No", {
845 872
846 873 
 test_that("get summary 1 Other:DDA", {
847 874 
   suppressWarnings({
875 
+    mock_input$BIO <- "Protein"
848 876 
     mock_input$filetype = "sample"
849 
-    mock_input$DDA_DIA <- "DDA"
877 
+    mock_input$DDA_DIA <- "LType"
878 
+    mock_input$LabelFreeType <- "DDA"
850 879 
     stub(getSummary1,"getData",mockGetData(mock_input))
851 880
852 881 
     output <- getSummary1(mock_input,getData(mock_input))
... ... 
@@ -878,8 +907,8 @@ stub(getSummary2,"remove_modal_spinner",{},depth=2)
878 907 
 test_that("get summary 2 PTM PTMTMT:Yes", {
879 908 
   suppressWarnings({
880 909 
     mock_input$filetype = "sample"
881 
-    mock_input$DDA_DIA <- "PTM"
882 
-    mock_input$PTMTMT <- "Yes"
910 
+    mock_input$BIO <- "PTM"
911 
+    mock_input$DDA_DIA <- "TMT"
883 912 
     stub(getSummary2,"getData",mockGetData(mock_input))
884 913
885 914 
     output <- getSummary2(mock_input,getData(mock_input))
... ... 
@@ -899,8 +928,8 @@ test_that("get summary 2 PTM PTMTMT:Yes", {
899 928 
 test_that("get summary 2 PTM PTMTMT:No", {
900 929 
   suppressWarnings({
901 930 
     mock_input$filetype = "sample"
902 
-    mock_input$DDA_DIA <- "PTM"
903 
-    mock_input$PTMTMT <- "No"
931 
+    mock_input$BIO <- "PTM"
932 
+    mock_input$DDA_DIA <- "LType"
904 933 
     stub(getSummary2,"getData",mockGetData(mock_input))
905 934
906 935 
     output <- getSummary2(mock_input,getData(mock_input))
... ... 
@@ -915,7 +944,9 @@ test_that("get summary 2 PTM PTMTMT:No", {
915 944 
 test_that("get summary 2 Other:DDA", {
916 945 
   suppressWarnings({
917 946 
     mock_input$filetype = "sample"
918 
-    mock_input$DDA_DIA <- "DDA"
947 
+    mock_input$BIO <- "Protein"
948 
+    mock_input$DDA_DIA <- "LType"
949 
+    mock_input$LabelFreeType <- "DDA"
919 950 
     stub(getSummary2,"getData",mockGetData(mock_input))
920 951
921 952 
     output <- getSummary2(mock_input,getData(mock_input))
... ... 
@@ -945,8 +976,8 @@ mockPreprocessData = function(mock_input) {
945 976 
 # err
946 977 
 test_that("preprocessData QC, PTM and PTMTMT: No", {
947 978 
   suppressWarnings({
948 
-    mock_input$DDA_DIA <- "PTM"
949 
-    mock_input$PTMTMT = "No"
979 
+    mock_input$BIO <- "PTM"
980 
+    mock_input$DDA_DIA <- "LType"
950 981 
     mock_input$filetype = "sample"
951 982 
     mock_input$norm = "equalizeMedians"
952 983 
     mock_input$log = "2"
... ... 
@@ -975,8 +1006,8 @@ test_that("preprocessData QC, PTM and PTMTMT: No", {
975 1006 
 # err
976 1007 
 test_that("preprocessData QC, PTM and PTMTMT: Yes", {
977 1008 
   suppressWarnings({
978 
-    mock_input$DDA_DIA <- "PTM"
979 
-    mock_input$PTMTMT = "Yes"
1009 
+    mock_input$BIO <- "PTM"
1010 
+    mock_input$DDA_DIA <- "TMT"
980 1011 
     mock_input$filetype = "sample"
981 1012 
     mock_input$norm = "equalizeMedians"
982 1013 
     mock_input$log = "2"
... ... 
@@ -1035,7 +1066,9 @@ test_that("preprocessData QC, PTM and PTMTMT: Yes", {
1035 1066 
 # err
1036 1067 
 test_that("preprocessData QC Other", {
1037 1068 
   suppressWarnings({
1038 
-    mock_input$DDA_DIA <- "DDA"
1069 
+    mock_input$BIO <- "Protein"
1070 
+    mock_input$DDA_DIA <- "LType"
1071 
+    mock_input$LabelFreeType <- "DDA"
1039 1072 
     mock_input$filetype = "sample"
1040 1073 
     mock_input$norm = "equalizeMedians"
1041 1074 
     mock_input$log = "2"
... ... 
@@ -1082,8 +1115,9 @@ test_that("get preprocessData code TMT & PTM", {
1082 1115 
     output <- preprocessDataCode(mock_input,mock_input)
1083 1116 
     expect_type(output,"character")
1084 1117
1085 
-    mock_input$DDA_DIA <- "PTM"
1086 
-    mock_input$PTMTMT <- "Yes"
1118 
+    mock_input$BIO <- "PTM"
1119 
+    mock_input$DDA_DIA <- "TMT"
1120 
+
1087 1121 
     stub(preprocessDataCode,"getDataCode","some test code")
1088 1122 
     stub(preprocessDataCode,"loadpage_input",mock_input)
1089 1123 
     stub(preprocessDataCode,"qc_input",mock_input)
... ... 
@@ -1091,7 +1125,8 @@ test_that("get preprocessData code TMT & PTM", {
1091 1125 
     output <- preprocessDataCode(mock_input,mock_input)
1092 1126 
     expect_type(output,"character")
1093 1127
1094 
-    mock_input$DDA_DIA <- "DDA"
1128 
+    mock_input$BIO <- "Protein"
1129 
+    mock_input$DDA_DIA <- "LType"
1095 1130 
     mock_input$features_used <- "all"
1096 1131 
     stub(preprocessDataCode,"getDataCode","some test code")
1097 1132 
     stub(preprocessDataCode,"loadpage_input",mock_input)
... ... 
@@ -1120,7 +1155,8 @@ test_that("dataComparison statmodel PTM PTMTMT: Yes", {
1120 1155 
     colnames(dummy_matrix) <- conditions
1121 1156 
     rownames(dummy_matrix) <- conditions
1122 1157
1123 
-    mock_input$DDA_DIA <- "PTM"
1158 
+    mock_input$BIO <- "PTM"
1159 
+    mock_input$DDA_DIA <- "TMT"
1124 1160 
     mock_input$PTMTMT = "Yes"
1125 1161 
     mock_input$filetype = "sample"
1126 1162 
     mock_input$summarization = "Median"
... ... 
@@ -1163,8 +1199,8 @@ test_that("dataComparison statmodel PTM PTMTMT: No", {
1163 1199 
     colnames(dummy_matrix) <- conditions
1164 1200 
     rownames(dummy_matrix) <- conditions
1165 1201
1166 
-    mock_input$DDA_DIA <- "PTM"
1167 
-    mock_input$PTMTMT = "No"
1202 
+    mock_input$BIO <- "PTM"
1203 
+    mock_input$DDA_DIA <- "LType"
1168 1204 
     mock_input$filetype = "sample"
1169 1205 
     mock_input$MBi = TRUE
1170 1206 
     mock_input$log = "2"
... ... 
@@ -1266,7 +1302,9 @@ test_that("dataComparison statmodel Other", {
1266 1302 
     colnames(dummy_matrix) <- conditions
1267 1303 
     rownames(dummy_matrix) <- conditions
1268 1304
1269 
-    mock_input$DDA_DIA <- "DDA"
1305 
+    mock_input$BIO <- "Protein"
1306 
+    mock_input$DDA_DIA <- "LType"
1307 
+    mock_input$LabelFreeType <- "DDA"
1270 1308 
     mock_input$filetype = "sample"
1271 1309 
     mock_input$norm = "equalizeMedians"
1272 1310 
     mock_input$log = "2"