1. pipeComp
  2. R
  3. scrna_utils.R
Browse code

fixed Misc change in Seurat

Pierre-Luc Germain authored on 09/06/2020 08:36:52
Showing 1 changed files
R/scrna_utils.R
History View file @ aff573a
... ... 
@@ -63,7 +63,7 @@ seWrap <- function(sce, min.cells=10, min.features=0){
63 63 
                             min.features=min.features,
64 64 
                             meta.data=as.data.frame(colData(sce)),
65 65 
                             project = "scRNAseq" )
66 
-  Misc(se)$rowData <- as.data.frame(rowData(sce))
66 
+  Misc(se, "rowData") <- as.data.frame(rowData(sce))
67 67 
   if("logcounts" %in%  assayNames(sce)){
68 68 
     se <- ScaleData(se, verbose = FALSE)
69 69 
     sce <- sce[row.names(se),]
... ... 
@@ -92,7 +92,7 @@ sceWrap <- function(seu) {
92 92 
     sce <- sce[row.names(norm),]
93 93 
     logcounts(sce) <- norm
94 94 
   }
95 
-  rowData(sce) <- Misc(seu)$rowData[row.names(sce),]
95 
+  rowData(sce) <- Misc(seu, "rowData")[row.names(sce),]
96 96 
   if(length(VariableFeatures(seu)))
97 97 
     metadata(sce)$VariableFeats <- VariableFeatures(seu)
98 98 
   if(length(Reductions(seu))>0){
Browse code

bioctyle changes

Pierre-Luc Germain authored on 12/05/2020 13:09:26
Showing 1 changed files
R/scrna_utils.R
History View file @ 886ad4f
... ... 
@@ -37,7 +37,7 @@ getDimensionality <- function(dat, method, maxDims=NULL){
37 37 
               pcaLocal.fan=pcaLocalDimEst(x, ver="fan"),
38 38 
               pcaLocal.maxgap=pcaLocalDimEst(x, ver="maxgap"),
39 39 
               maxLikGlobal=maxLikGlobalDimEst(x, k=20, unbiased=TRUE),
40 
-	      maxLikGlobal10=maxLikGlobalDimEst(x, k=10, unbiased=TRUE),
40 
+              maxLikGlobal10=maxLikGlobalDimEst(x, k=10, unbiased=TRUE),
41 41 
               pcaOtpmPointwise.max=pcaOtpmPointwiseDimEst(x,N=10),
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               elbow=farthestPoint(sdv)-1,
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               ifelse( !is.function(method) &&
Browse code

Merge branch 'master' into devel

Pierre-Luc Germain authored on 12/05/2020 11:52:12
Showing 0 changed files
Browse code

changed all @ to accessors

Pierre-Luc Germain authored on 12/05/2020 10:42:48
Showing 1 changed files
R/scrna_utils.R
History View file @ b04a719
... ... 
@@ -15,7 +15,7 @@ getDimensionality <- function(dat, method, maxDims=NULL){
15 15 
   if(is.numeric(method) || grepl("^[0-9]+$", method))
16 16 
     return(as.integer(round(as.numeric(method))))
17 17 
   if(is(dat, "Seurat")){
18 
-    x <- dat[["pca"]]@cell.embeddings
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+    x <- Embeddings(dat[["pca"]])
19 19 
     sdv <- Stdev(dat, "pca")
20 20 
   } else {
21 21 
     if(method=="jackstraw.elbow")
... ... 
@@ -62,10 +62,10 @@ seWrap <- function(sce, min.cells=10, min.features=0){
62 62 
                             min.features=min.features,
63 63 
                             meta.data=as.data.frame(colData(sce)),
64 64 
                             project = "scRNAseq" )
65 
-  se@misc$rowData <- as.data.frame(rowData(sce))
65 
+  Misc(se)$rowData <- as.data.frame(rowData(sce))
66 66 
   if("logcounts" %in%  assayNames(sce)){
67 67 
     se <- ScaleData(se, verbose = FALSE)
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-    se@assays$RNA@data <- logcounts(sce)
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+    se <- SetAssayData(se, slot="data", new.data=logcounts(sce))
69 69 
   }
70 70 
   if(!is.null(metadata(sce)$VariableFeats))
71 71 
     VariableFeatures(se) <- metadata(sce)$VariableFeats
... ... 
@@ -89,12 +89,11 @@ sceWrap <- function(seu) {
89 89 
     sce <- sce[row.names(norm),]
90 90 
     logcounts(sce) <- norm
91 91 
   }
92 
-  rowData(sce) <- seu@misc$rowData[row.names(sce),]
92 
+  rowData(sce) <- Misc(seu)$rowData[row.names(sce),]
93 93 
   if(length(VariableFeatures(seu)))
94 94 
     metadata(sce)$VariableFeats <- VariableFeatures(seu)
95 95 
   if(length(Reductions(seu))>0){
96 
-    reducedDims(sce) <- lapply( seu@reductions,
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-                                FUN=function(x) [email protected] )
96 
+    reducedDims(sce) <- lapply( Reductions(seu), FUN=Embeddings )
98 97 
   }
99 98 
   sce
100 99 
 }
Browse code

replaced @ with accessors

plger authored on 12/05/2020 09:15:55
Showing 1 changed files
R/scrna_utils.R
History View file @ 5b7d35d
... ... 
@@ -37,6 +37,7 @@ getDimensionality <- function(dat, method, maxDims=NULL){
37 37 
               pcaLocal.fan=pcaLocalDimEst(x, ver="fan"),
38 38 
               pcaLocal.maxgap=pcaLocalDimEst(x, ver="maxgap"),
39 39 
               maxLikGlobal=maxLikGlobalDimEst(x, k=20, unbiased=TRUE),
40 
+	      maxLikGlobal10=maxLikGlobalDimEst(x, k=10, unbiased=TRUE),
40 41 
               pcaOtpmPointwise.max=pcaOtpmPointwiseDimEst(x,N=10),
41 42 
               elbow=farthestPoint(sdv)-1,
42 43 
               ifelse( !is.function(method) &&
... ... 
@@ -65,7 +66,9 @@ seWrap <- function(sce, min.cells=10, min.features=0){
65 66 
   se@misc$rowData <- as.data.frame(rowData(sce))
66 67 
   if("logcounts" %in%  assayNames(sce)){
67 68 
     se <- ScaleData(se, verbose = FALSE)
68 
-    se@assays$RNA@data <- logcounts(sce)
69 
+    sce <- sce[row.names(se),]
70 
+    se <- SetAssayData(se, slot="data", new.data=logcounts(sce))
71 
+    se <- SetAssayData(se, slot="scale.data", new.data=logcounts(sce))
69 72 
   }
70 73 
   if(!is.null(metadata(sce)$VariableFeats))
71 74 
     VariableFeatures(se) <- metadata(sce)$VariableFeats
Browse code

modified getDimensionality to accept the dim directly

plger authored on 01/05/2020 07:14:46
Showing 1 changed files
R/scrna_utils.R
History View file @ 9f02de9
... ... 
@@ -12,6 +12,8 @@
12 12 
 #' @importFrom SingleCellExperiment reducedDim
13 13 
 #' @import intrinsicDimension
14 14 
 getDimensionality <- function(dat, method, maxDims=NULL){
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+  if(is.numeric(method) || grepl("^[0-9]+$", method))
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+    return(as.integer(round(as.numeric(method))))
15 17 
   if(is(dat, "Seurat")){
16 18 
     x <- dat[["pca"]]@cell.embeddings
17 19 
     sdv <- Stdev(dat, "pca")
Browse code

fixed non-imported dependencies, added documentation

Pierre-Luc Germain authored on 01/04/2020 16:29:43
Showing 1 changed files
R/scrna_utils.R
History View file @ 20c0681
... ... 
@@ -55,7 +55,6 @@ getDimensionality <- function(dat, method, maxDims=NULL){
55 55 
 seWrap <- function(sce, min.cells=10, min.features=0){
56 56 
   if(is(sce,"Seurat")) return(sce)
57 57 
   if(!is(sce,"SingleCellExperiment")) stop("not a SingleCellExperiment!")
58 
-  suppressPackageStartupMessages(library(Seurat))
59 58 
   se <- CreateSeuratObject( counts=counts(sce),
60 59 
                             min.cells=min.cells,
61 60 
                             min.features=min.features,
Browse code

moved metadata generation fns back to extdata scripts

Pierre-Luc Germain authored on 01/04/2020 09:08:56
Showing 1 changed files
R/scrna_utils.R
History View file @ 4e9c4fd
... ... 
@@ -54,6 +54,7 @@ getDimensionality <- function(dat, method, maxDims=NULL){
54 54 
 #' @importFrom SummarizedExperiment assayNames
55 55 
 seWrap <- function(sce, min.cells=10, min.features=0){
56 56 
   if(is(sce,"Seurat")) return(sce)
57 
+  if(!is(sce,"SingleCellExperiment")) stop("not a SingleCellExperiment!")
57 58 
   suppressPackageStartupMessages(library(Seurat))
58 59 
   se <- CreateSeuratObject( counts=counts(sce),
59 60 
                             min.cells=min.cells,
... ... 
@@ -78,10 +79,8 @@ seWrap <- function(sce, min.cells=10, min.features=0){
78 79 
 #' @import SingleCellExperiment Seurat
79 80 
 #' @importFrom SummarizedExperiment rowData<-
80 81 
 sceWrap <- function(seu) {
81 
-  suppressPackageStartupMessages({
82 
-    library(SingleCellExperiment)
83 
-    library(Seurat)
84 
-  })
82 
+  if(is(seu,"SingleCellExperiment")) return(seu)
83 
+  if(!is(seu,"Seurat")) stop("not a Seurat object!")
85 84 
   sce <- SingleCellExperiment(
86 85 
     list(counts=GetAssayData(seu, assay="RNA", slot="counts")),
87 86 
     colData = seu[[]] )
Browse code

code formatting for bioc...

Pierre-Luc Germain authored on 01/04/2020 06:41:32
Showing 1 changed files
R/scrna_utils.R
History View file @ a53f122
... ... 
@@ -51,6 +51,7 @@ getDimensionality <- function(dat, method, maxDims=NULL){
51 51 
 # sce2se conversion
52 52 
 # not exported
53 53 
 #' @import SingleCellExperiment Seurat
54 
+#' @importFrom SummarizedExperiment assayNames
54 55 
 seWrap <- function(sce, min.cells=10, min.features=0){
55 56 
   if(is(sce,"Seurat")) return(sce)
56 57 
   suppressPackageStartupMessages(library(Seurat))
... ... 
@@ -75,13 +76,15 @@ seWrap <- function(sce, min.cells=10, min.features=0){
75 76 
 # se2sce conversion
76 77 
 # not exported
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 #' @import SingleCellExperiment Seurat
79 
+#' @importFrom SummarizedExperiment rowData<-
78 80 
 sceWrap <- function(seu) {
79 81 
   suppressPackageStartupMessages({
80 82 
     library(SingleCellExperiment)
81 83 
     library(Seurat)
82 84 
   })
83 
-  sce <- SingleCellExperiment(list(counts=GetAssayData(seu, assay="RNA", slot="counts")),
84 
-                              colData = seu[[]])
85 
+  sce <- SingleCellExperiment(
86 
+    list(counts=GetAssayData(seu, assay="RNA", slot="counts")),
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+    colData = seu[[]] )
85 88 
   if(nrow(norm <- GetAssayData(seu, slot="scale.data"))>0){
86 89 
     sce <- sce[row.names(norm),]
87 90 
     logcounts(sce) <- norm
... ... 
@@ -90,7 +93,8 @@ sceWrap <- function(seu) {
90 93 
   if(length(VariableFeatures(seu)))
91 94 
     metadata(sce)$VariableFeats <- VariableFeatures(seu)
92 95 
   if(length(Reductions(seu))>0){
93 
-    reducedDims(sce) <- lapply(seu@reductions, FUN=function(x) [email protected])
96 
+    reducedDims(sce) <- lapply( seu@reductions,
97 
+                                FUN=function(x) [email protected] )
94 98 
   }
95 99 
   sce
96 100 
 }
Browse code

more modifs for bioc standards...

Pierre-Luc Germain authored on 31/03/2020 18:11:10
Showing 1 changed files
R/scrna_utils.R
History View file @ 36e3057
... ... 
@@ -2,8 +2,8 @@
2 2 
 #'
3 3 
 #' Returns the estimated intrinsic dimensionality of a dataset.
4 4 
 #'
5 
-#' @param dat A Seurat or SCE object
6 
-#' @param method The dimensionality method to use
5 
+#' @param dat A Seurat or SCE object with a pca embedding.
6 
+#' @param method The dimensionality method to use.
7 7 
 #' @param maxDims Deprecated and ignored.
8 8 
 #'
9 9 
 #' @return An integer.
Browse code

changes for bioc standards

Pierre-Luc Germain authored on 30/03/2020 18:53:25
Showing 1 changed files
R/scrna_utils.R
History View file @ 3fceaac
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,96 @@
1 
+#' getDimensionality
2 
+#'
3 
+#' Returns the estimated intrinsic dimensionality of a dataset.
4 
+#'
5 
+#' @param dat A Seurat or SCE object
6 
+#' @param method The dimensionality method to use
7 
+#' @param maxDims Deprecated and ignored.
8 
+#'
9 
+#' @return An integer.
10 
+#'
11 
+#' @importFrom Seurat Stdev
12 
+#' @importFrom SingleCellExperiment reducedDim
13 
+#' @import intrinsicDimension
14 
+getDimensionality <- function(dat, method, maxDims=NULL){
15 
+  if(is(dat, "Seurat")){
16 
+    x <- dat[["pca"]]@cell.embeddings
17 
+    sdv <- Stdev(dat, "pca")
18 
+  } else {
19 
+    if(method=="jackstraw.elbow")
20 
+      stop("the jackstraw.elbow method is only available for Seurat objects.")
21 
+    x <- reducedDim(dat, "PCA")
22 
+    sdv <- attr(reducedDim(dat, "PCA"), "percentVar")
23 
+  }
24 
+  # conversion for backward compatibility:
25 
+  conv <- c( "fisherSeparability"="FisherSeparability",
26 
+             "scran.denoisePCA"="scran.ndims.wrapper",
27 
+             "jackstraw.elbow"="js.wrapper"
28 
+  )
29 
+  if(method %in% names(conv)) method <- as.character(conv[method])
30 
+
31 
+  x <- switch(method,
32 
+              essLocal.a=essLocalDimEst(x),
33 
+              essLocal.b=essLocalDimEst(x, ver="b"),
34 
+              pcaLocal.FO=pcaLocalDimEst(x,ver="FO"),
35 
+              pcaLocal.fan=pcaLocalDimEst(x, ver="fan"),
36 
+              pcaLocal.maxgap=pcaLocalDimEst(x, ver="maxgap"),
37 
+              maxLikGlobal=maxLikGlobalDimEst(x, k=20, unbiased=TRUE),
38 
+              pcaOtpmPointwise.max=pcaOtpmPointwiseDimEst(x,N=10),
39 
+              elbow=farthestPoint(sdv)-1,
40 
+              ifelse( !is.function(method) &&
41 
+                        !( is.character(method) &&
42 
+                             is.function(method <- get(method)) ),
43 
+                      stop("Unknown dimensionality method!"),
44 
+                      method(dat) )
45 
+  )
46 
+  if(is.list(x) && "dim.est" %in% names(x)) x <- max(x$dim.est)
47 
+  as.integer(round(x))
48 
+}
49 
+
50 
+
51 
+# sce2se conversion
52 
+# not exported
53 
+#' @import SingleCellExperiment Seurat
54 
+seWrap <- function(sce, min.cells=10, min.features=0){
55 
+  if(is(sce,"Seurat")) return(sce)
56 
+  suppressPackageStartupMessages(library(Seurat))
57 
+  se <- CreateSeuratObject( counts=counts(sce),
58 
+                            min.cells=min.cells,
59 
+                            min.features=min.features,
60 
+                            meta.data=as.data.frame(colData(sce)),
61 
+                            project = "scRNAseq" )
62 
+  se@misc$rowData <- as.data.frame(rowData(sce))
63 
+  if("logcounts" %in%  assayNames(sce)){
64 
+    se <- ScaleData(se, verbose = FALSE)
65 
+    se@assays$RNA@data <- logcounts(sce)
66 
+  }
67 
+  if(!is.null(metadata(sce)$VariableFeats))
68 
+    VariableFeatures(se) <- metadata(sce)$VariableFeats
69 
+  if(length(reducedDimNames(sce)) != 0)
70 
+    se[["pca"]] <- CreateDimReducObject(embeddings=reducedDim(sce), key="PC_",
71 
+                                        assay="RNA")
72 
+  se
73 
+}
74 
+
75 
+# se2sce conversion
76 
+# not exported
77 
+#' @import SingleCellExperiment Seurat
78 
+sceWrap <- function(seu) {
79 
+  suppressPackageStartupMessages({
80 
+    library(SingleCellExperiment)
81 
+    library(Seurat)
82 
+  })
83 
+  sce <- SingleCellExperiment(list(counts=GetAssayData(seu, assay="RNA", slot="counts")),
84 
+                              colData = seu[[]])
85 
+  if(nrow(norm <- GetAssayData(seu, slot="scale.data"))>0){
86 
+    sce <- sce[row.names(norm),]
87 
+    logcounts(sce) <- norm
88 
+  }
89 
+  rowData(sce) <- seu@misc$rowData[row.names(sce),]
90 
+  if(length(VariableFeatures(seu)))
91 
+    metadata(sce)$VariableFeats <- VariableFeatures(seu)
92 
+  if(length(Reductions(seu))>0){
93 
+    reducedDims(sce) <- lapply(seu@reductions, FUN=function(x) [email protected])
94 
+  }
95 
+  sce
96 
+}