1. singleCellTK
  2. man
  3. plotTSNE.Rd
Browse code

Deprecate `getTSNE`, add `runTSNE` and `runQuickTSNE`

Yichen Wang authored on 28/09/2022 06:39:03
Showing 1 changed files
man/plotTSNE.Rd
History View file @ 27e3c620
... ... 
@@ -10,7 +10,7 @@ plotTSNE(
10 10 
   shape = NULL,
11 11 
   reducedDimName = "TSNE",
12 12 
   runTSNE = FALSE,
13 
-  useAssay = "logcounts"
13 
+  useAssay = "counts"
14 14 
 )
15 15 
 }
16 16 
 \arguments{
Browse code

Fix check errors

Yichen Wang authored on 28/06/2022 22:07:14
Showing 1 changed files
man/plotTSNE.Rd
History View file @ f0b0d74b
... ... 
@@ -39,5 +39,4 @@ Plot t-SNE plot on dimensionality reduction data run from t-SNE method.
39 39 
 data("mouseBrainSubsetSCE")
40 40 
 plotTSNE(mouseBrainSubsetSCE, colorBy = "level1class",
41 41 
          reducedDimName = "TSNE_counts")
42 
-
43 42 
 }
Browse code

Added more unit tests

Yichen Wang authored on 28/06/2022 20:51:30
Showing 1 changed files
man/plotTSNE.Rd
History View file @ 976db869
... ... 
@@ -6,8 +6,8 @@
6 6 
 \usage{
7 7 
 plotTSNE(
8 8 
   inSCE,
9 
-  colorBy = "No Color",
10 
-  shape = "No Shape",
9 
+  colorBy = NULL,
10 
+  shape = NULL,
11 11 
   reducedDimName = "TSNE",
12 12 
   runTSNE = FALSE,
13 13 
   useAssay = "logcounts"
Browse code

Removed SCtkExperiment class and methods. Removed all references in the documentation

Joshua D. Campbell authored on 02/07/2020 04:10:40
Showing 1 changed files
man/plotTSNE.Rd
History View file @ 3fcae1c4
... ... 
@@ -14,7 +14,7 @@ plotTSNE(
14 14 
 )
15 15 
 }
16 16 
 \arguments{
17 
-\item{inSCE}{Input SCtkExperiment object. Required}
17 
+\item{inSCE}{Input \linkS4class{SingleCellExperiment} object.}
18 18
19 19 
 \item{colorBy}{color by condition.}
20 20
Browse code

Updated LIGER function and put correct dependencies in DESCRIPTION. Updated docs

Joshua D. Campbell authored on 06/03/2020 05:15:13
Showing 1 changed files
man/plotTSNE.Rd
History View file @ 64d3a71f
... ... 
@@ -4,8 +4,14 @@
4 4 
 \alias{plotTSNE}
5 5 
 \title{Plot t-SNE plot on dimensionality reduction data run from t-SNE method.}
6 6 
 \usage{
7 
-plotTSNE(inSCE, colorBy = "No Color", shape = "No Shape",
8 
-  reducedDimName = "TSNE", runTSNE = FALSE, useAssay = "logcounts")
7 
+plotTSNE(
8 
+  inSCE,
9 
+  colorBy = "No Color",
10 
+  shape = "No Shape",
11 
+  reducedDimName = "TSNE",
12 
+  runTSNE = FALSE,
13 
+  useAssay = "logcounts"
14 
+)
9 15 
 }
10 16 
 \arguments{
11 17 
 \item{inSCE}{Input SCtkExperiment object. Required}
Browse code

move to branch

Yichen Wang authored on 04/03/2020 20:32:17
Showing 1 changed files
man/plotTSNE.Rd
History View file @ e624033d
... ... 
@@ -4,14 +4,8 @@
4 4 
 \alias{plotTSNE}
5 5 
 \title{Plot t-SNE plot on dimensionality reduction data run from t-SNE method.}
6 6 
 \usage{
7 
-plotTSNE(
8 
-  inSCE,
9 
-  colorBy = "No Color",
10 
-  shape = "No Shape",
11 
-  reducedDimName = "TSNE",
12 
-  runTSNE = FALSE,
13 
-  useAssay = "logcounts"
14 
-)
7 
+plotTSNE(inSCE, colorBy = "No Color", shape = "No Shape",
8 
+  reducedDimName = "TSNE", runTSNE = FALSE, useAssay = "logcounts")
15 9 
 }
16 10 
 \arguments{
17 11 
 \item{inSCE}{Input SCtkExperiment object. Required}
Browse code

Fixed errors/warnings in DoubletFinder code. Updated docs. Added documentation for importCellRangerV2/V3Sample functions. Added install of DoubletFinder from github in DESCRIPTION and in .travis.yml

Joshua D. Campbell authored on 15/02/2020 00:05:10
Showing 1 changed files
man/plotTSNE.Rd
History View file @ 8a33a64b
... ... 
@@ -4,8 +4,14 @@
4 4 
 \alias{plotTSNE}
5 5 
 \title{Plot t-SNE plot on dimensionality reduction data run from t-SNE method.}
6 6 
 \usage{
7 
-plotTSNE(inSCE, colorBy = "No Color", shape = "No Shape",
8 
-  reducedDimName = "TSNE", runTSNE = FALSE, useAssay = "logcounts")
7 
+plotTSNE(
8 
+  inSCE,
9 
+  colorBy = "No Color",
10 
+  shape = "No Shape",
11 
+  reducedDimName = "TSNE",
12 
+  runTSNE = FALSE,
13 
+  useAssay = "logcounts"
14 
+)
9 15 
 }
10 16 
 \arguments{
11 17 
 \item{inSCE}{Input SCtkExperiment object. Required}
Browse code

Create new documentation

Yusuke Koga authored on 17/01/2020 15:37:00
Showing 1 changed files
man/plotTSNE.Rd
History View file @ 4669c011
... ... 
@@ -4,14 +4,8 @@
4 4 
 \alias{plotTSNE}
5 5 
 \title{Plot t-SNE plot on dimensionality reduction data run from t-SNE method.}
6 6 
 \usage{
7 
-plotTSNE(
8 
-  inSCE,
9 
-  colorBy = "No Color",
10 
-  shape = "No Shape",
11 
-  reducedDimName = "TSNE",
12 
-  runTSNE = FALSE,
13 
-  useAssay = "logcounts"
14 
-)
7 
+plotTSNE(inSCE, colorBy = "No Color", shape = "No Shape",
8 
+  reducedDimName = "TSNE", runTSNE = FALSE, useAssay = "logcounts")
15 9 
 }
16 10 
 \arguments{
17 11 
 \item{inSCE}{Input SCtkExperiment object. Required}
Browse code

add import and QC functions

87875172 authored on 18/12/2019 15:45:52
Showing 1 changed files
man/plotTSNE.Rd
History View file @ b5989368
... ... 
@@ -4,8 +4,14 @@
4 4 
 \alias{plotTSNE}
5 5 
 \title{Plot t-SNE plot on dimensionality reduction data run from t-SNE method.}
6 6 
 \usage{
7 
-plotTSNE(inSCE, colorBy = "No Color", shape = "No Shape",
8 
-  reducedDimName = "TSNE", runTSNE = FALSE, useAssay = "logcounts")
7 
+plotTSNE(
8 
+  inSCE,
9 
+  colorBy = "No Color",
10 
+  shape = "No Shape",
11 
+  reducedDimName = "TSNE",
12 
+  runTSNE = FALSE,
13 
+  useAssay = "logcounts"
14 
+)
9 15 
 }
10 16 
 \arguments{
11 17 
 \item{inSCE}{Input SCtkExperiment object. Required}
Browse code

removed duplicates which came up due to @describeIn section from dependent PCA, tSNE methods

Mohammed Muzamil Khan authored on 29/03/2019 19:11:25
Showing 1 changed files
man/plotTSNE.Rd
History View file @ a7648e0a
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,37 @@
1 
+% Generated by roxygen2: do not edit by hand
2 
+% Please edit documentation in R/plotTSNE.R
3 
+\name{plotTSNE}
4 
+\alias{plotTSNE}
5 
+\title{Plot t-SNE plot on dimensionality reduction data run from t-SNE method.}
6 
+\usage{
7 
+plotTSNE(inSCE, colorBy = "No Color", shape = "No Shape",
8 
+  reducedDimName = "TSNE", runTSNE = FALSE, useAssay = "logcounts")
9 
+}
10 
+\arguments{
11 
+\item{inSCE}{Input SCtkExperiment object. Required}
12 
+
13 
+\item{colorBy}{color by condition.}
14 
+
15 
+\item{shape}{add shape to each distinct label.}
16 
+
17 
+\item{reducedDimName}{a name to store the results of the dimension reduction
18 
+coordinates obtained from this method. This is stored in the SingleCellExperiment
19 
+object in the reducedDims slot. Required.}
20 
+
21 
+\item{runTSNE}{Run t-SNE if the reducedDimName does not exist. the Default is
22 
+FALSE.}
23 
+
24 
+\item{useAssay}{Indicate which assay to use. The default is "logcounts".}
25 
+}
26 
+\value{
27 
+A t-SNE plot
28 
+}
29 
+\description{
30 
+Plot t-SNE plot on dimensionality reduction data run from t-SNE method.
31 
+}
32 
+\examples{
33 
+data("mouseBrainSubsetSCE")
34 
+plotTSNE(mouseBrainSubsetSCE, colorBy = "level1class",
35 
+         reducedDimName = "TSNE_counts")
36 
+
37 
+}
Browse code

Consistent use of inSCE to refer to the input SCtkExperiment object. Combined documentation for functions with similar functionality. Version bump

David Jenkins authored on 12/04/2018 22:21:24
Showing 1 changed files
man/plotTSNE.Rd
History View file @ 0be6f650
1 1 
deleted file mode 100644
... ... 
@@ -1,37 +0,0 @@
1 
-% Generated by roxygen2: do not edit by hand
2 
-% Please edit documentation in R/plotTSNE.R
3 
-\name{plotTSNE}
4 
-\alias{plotTSNE}
5 
-\title{Plot t-SNE}
6 
-\usage{
7 
-plotTSNE(countData, colorBy = "No Color", shape = "No Shape",
8 
-  reducedDimName = "TSNE", runTSNE = FALSE, useAssay = "logcounts")
9 
-}
10 
-\arguments{
11 
-\item{countData}{A SCE object}
12 
-
13 
-\item{colorBy}{The variable to color clusters by}
14 
-
15 
-\item{shape}{Shape of the points}
16 
-
17 
-\item{reducedDimName}{t-SNE dimension name. The default is TSNE
18 
-The toolkit will store data with the pattern <ASSAY>_<ALGORITHM>.}
19 
-
20 
-\item{runTSNE}{Run t-SNE if the reducedDimName does not exist. the Default is
21 
-FALSE.}
22 
-
23 
-\item{useAssay}{Indicate which assay to use for t-SNE if you are running it.
24 
-Default is "counts"}
25 
-}
26 
-\value{
27 
-A t-SNE plot
28 
-}
29 
-\description{
30 
-Use this function to plot t-SNE results
31 
-}
32 
-\examples{
33 
-data("mouseBrainSubsetSCE")
34 
-plotTSNE(mouseBrainSubsetSCE, colorBy = "level1class",
35 
-         reducedDimName = "TSNE_counts")
36 
-
37 
-}
Browse code

Consistent use of camel case throughout the app

David Jenkins authored on 06/04/2018 20:11:01
Showing 1 changed files
man/plotTSNE.Rd
History View file @ c32ed94f
... ... 
@@ -4,11 +4,11 @@
4 4 
 \alias{plotTSNE}
5 5 
 \title{Plot t-SNE}
6 6 
 \usage{
7 
-plotTSNE(count_data, colorBy = "No Color", shape = "No Shape",
8 
-  reducedDimName = "TSNE", runTSNE = FALSE, use_assay = "logcounts")
7 
+plotTSNE(countData, colorBy = "No Color", shape = "No Shape",
8 
+  reducedDimName = "TSNE", runTSNE = FALSE, useAssay = "logcounts")
9 9 
 }
10 10 
 \arguments{
11 
-\item{count_data}{A SCE object}
11 
+\item{countData}{A SCE object}
12 12
13 13 
 \item{colorBy}{The variable to color clusters by}
14 14
... ... 
@@ -20,7 +20,7 @@ The toolkit will store data with the pattern <ASSAY>_<ALGORITHM>.}
20 20 
 \item{runTSNE}{Run t-SNE if the reducedDimName does not exist. the Default is
21 21 
 FALSE.}
22 22
23 
-\item{use_assay}{Indicate which assay to use for t-SNE if you are running it.
23 
+\item{useAssay}{Indicate which assay to use for t-SNE if you are running it.
24 24 
 Default is "counts"}
25 25 
 }
26 26 
 \value{
... ... 
@@ -30,8 +30,8 @@ A t-SNE plot
30 30 
 Use this function to plot t-SNE results
31 31 
 }
32 32 
 \examples{
33 
-data("mouse_brain_subset_sce")
34 
-plotTSNE(mouse_brain_subset_sce, colorBy = "level1class",
33 
+data("mouseBrainSubsetSCE")
34 
+plotTSNE(mouseBrainSubsetSCE, colorBy = "level1class",
35 35 
          reducedDimName = "TSNE_counts")
36 36
37 37 
 }
Browse code

Removed examples that weren't being used. Updated requirement to 3.5 for bioconductor release, changednged the name of the GSE60361 dataset to be more descriptive. Added a link to the data source. Fixed DESeq2 bug. Version bump

David Jenkins authored on 20/03/2018 23:51:57
Showing 1 changed files
man/plotTSNE.Rd
History View file @ 50eb6908
... ... 
@@ -30,8 +30,8 @@ A t-SNE plot
30 30 
 Use this function to plot t-SNE results
31 31 
 }
32 32 
 \examples{
33 
-data("GSE60361_subset_sce")
34 
-plotTSNE(GSE60361_subset_sce, colorBy = "level1class",
33 
+data("mouse_brain_subset_sce")
34 
+plotTSNE(mouse_brain_subset_sce, colorBy = "level1class",
35 35 
          reducedDimName = "TSNE_counts")
36 36
37 37 
 }
Browse code

Added runnable examples to more functions

David Jenkins authored on 20/02/2018 02:44:56
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man/plotTSNE.Rd
History View file @ 443bc2c7
... ... 
@@ -29,3 +29,9 @@ A t-SNE plot
29 29 
 \description{
30 30 
 Use this function to plot t-SNE results
31 31 
 }
32 
+\examples{
33 
+data("GSE60361_subset_sce")
34 
+plotTSNE(GSE60361_subset_sce, colorBy = "level1class",
35 
+         reducedDimName = "TSNE_counts")
36 
+
37 
+}
Browse code

Spell check

David Jenkins authored on 12/12/2017 22:11:05
Showing 1 changed files
man/plotTSNE.Rd
History View file @ 8d72aa93
... ... 
@@ -2,7 +2,7 @@
2 2 
 % Please edit documentation in R/plotTSNE.R
3 3 
 \name{plotTSNE}
4 4 
 \alias{plotTSNE}
5 
-\title{Plot TSNE}
5 
+\title{Plot t-SNE}
6 6 
 \usage{
7 7 
 plotTSNE(count_data, colorBy = "No Color", shape = "No Shape",
8 8 
   reducedDimName = "TSNE", runTSNE = FALSE, use_assay = "logcounts")
... ... 
@@ -14,18 +14,18 @@ plotTSNE(count_data, colorBy = "No Color", shape = "No Shape",
14 14
15 15 
 \item{shape}{Shape of the points}
16 16
17 
-\item{reducedDimName}{TSNE dimension name. The default is PCA.
18 
-The toolkit will store data with the pattern <ASSSAY>_<ALGORITHM>.}
17 
+\item{reducedDimName}{t-SNE dimension name. The default is TSNE
18 
+The toolkit will store data with the pattern <ASSAY>_<ALGORITHM>.}
19 19
20 
-\item{runTSNE}{Run t-SNE if the reducedDimName doesn't exist. the Default is
20 
+\item{runTSNE}{Run t-SNE if the reducedDimName does not exist. the Default is
21 21 
 FALSE.}
22 22
23 23 
 \item{use_assay}{Indicate which assay to use for t-SNE if you are running it.
24 24 
 Default is "counts"}
25 25 
 }
26 26 
 \value{
27 
-A TSNE plot
27 
+A t-SNE plot
28 28 
 }
29 29 
 \description{
30 
-Use this function to plot PCA or tSNE results
30 
+Use this function to plot t-SNE results
31 31 
 }
Browse code

Changed default behavior of plot functions to not run the dimred because of time concerns. Linted some code

David Jenkins authored on 22/10/2017 23:25:10
Showing 1 changed files
man/plotTSNE.Rd
History View file @ 7827e2ef
... ... 
@@ -5,7 +5,7 @@
5 5 
 \title{Plot TSNE}
6 6 
 \usage{
7 7 
 plotTSNE(count_data, colorBy = "No Color", shape = "No Shape",
8 
-  use_assay = "logcounts", reducedDimName = "TSNE")
8 
+  reducedDimName = "TSNE", runTSNE = FALSE, use_assay = "logcounts")
9 9 
 }
10 10 
 \arguments{
11 11 
 \item{count_data}{A SCE object}
... ... 
@@ -14,10 +14,14 @@ plotTSNE(count_data, colorBy = "No Color", shape = "No Shape",
14 14
15 15 
 \item{shape}{Shape of the points}
16 16
17 
-\item{use_assay}{Indicate which assay to use for PCA. Default is "counts"}
18 
-
19 17 
 \item{reducedDimName}{TSNE dimension name. The default is PCA.
20 18 
 The toolkit will store data with the pattern <ASSSAY>_<ALGORITHM>.}
19 
+
20 
+\item{runTSNE}{Run t-SNE if the reducedDimName doesn't exist. the Default is
21 
+FALSE.}
22 
+
23 
+\item{use_assay}{Indicate which assay to use for t-SNE if you are running it.
24 
+Default is "counts"}
21 25 
 }
22 26 
 \value{
23 27 
 A TSNE plot
Browse code

Added UI elements for combat tab. Ran devtools::document()

David Jenkins authored on 19/10/2017 21:43:57
Showing 1 changed files
man/plotTSNE.Rd
History View file @ 1eeca134
... ... 
@@ -5,7 +5,7 @@
5 5 
 \title{Plot TSNE}
6 6 
 \usage{
7 7 
 plotTSNE(count_data, colorBy = "No Color", shape = "No Shape",
8 
-  use_assay = "counts", reducedDimName = "TSNE")
8 
+  use_assay = "logcounts", reducedDimName = "TSNE")
9 9 
 }
10 10 
 \arguments{
11 11 
 \item{count_data}{A SCE object}
Browse code

Support for choosing availabe assays on dimred tab

David Jenkins authored on 19/10/2017 20:54:23
Showing 1 changed files
man/plotTSNE.Rd
History View file @ cb9afbc1
... ... 
@@ -4,7 +4,8 @@
4 4 
 \alias{plotTSNE}
5 5 
 \title{Plot TSNE}
6 6 
 \usage{
7 
-plotTSNE(count_data, colorBy = "No Color", shape = "No Shape")
7 
+plotTSNE(count_data, colorBy = "No Color", shape = "No Shape",
8 
+  use_assay = "counts", reducedDimName = "TSNE")
8 9 
 }
9 10 
 \arguments{
10 11 
 \item{count_data}{A SCE object}
... ... 
@@ -12,6 +13,11 @@ plotTSNE(count_data, colorBy = "No Color", shape = "No Shape")
12 13 
 \item{colorBy}{The variable to color clusters by}
13 14
14 15 
 \item{shape}{Shape of the points}
16 
+
17 
+\item{use_assay}{Indicate which assay to use for PCA. Default is "counts"}
18 
+
19 
+\item{reducedDimName}{TSNE dimension name. The default is PCA.
20 
+The toolkit will store data with the pattern <ASSSAY>_<ALGORITHM>.}
15 21 
 }
16 22 
 \value{
17 23 
 A TSNE plot
Browse code

Modified the underlaying object by extending the SingleCellExperiment to a SingleCelltkExperiment that stores PCA percent variances within the function. Modifications to the plotting and getting of PCA and TSNE functions to support the new object. Updated the example objects to SingleCelltkExperiment objects

David Jenkins authored on 12/09/2017 23:38:53
Showing 1 changed files
man/plotTSNE.Rd
History View file @ 9806bb6f
... ... 
@@ -4,14 +4,11 @@
4 4 
 \alias{plotTSNE}
5 5 
 \title{Plot TSNE}
6 6 
 \usage{
7 
-plotTSNE(count_data, tsne_df = NULL, colorBy = "No Color",
8 
-  shape = "No Shape")
7 
+plotTSNE(count_data, colorBy = "No Color", shape = "No Shape")
9 8 
 }
10 9 
 \arguments{
11 10 
 \item{count_data}{A SCE object}
12 11
13 
-\item{tsne_df}{tSNE data frame}
14 
-
15 12 
 \item{colorBy}{The variable to color clusters by}
16 13
17 14 
 \item{shape}{Shape of the points}
Browse code

Documentation update and modified diffex to SingleCellExperiment

David Jenkins authored on 08/08/2017 20:20:51
Showing 1 changed files
man/plotTSNE.Rd
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... ... 
@@ -4,7 +4,8 @@
4 4 
 \alias{plotTSNE}
5 5 
 \title{Plot TSNE}
6 6 
 \usage{
7 
-plotTSNE(count_data, tsne_df = NULL, colorBy = NULL, shape = NULL)
7 
+plotTSNE(count_data, tsne_df = NULL, colorBy = "No Color",
8 
+  shape = "No Shape")
8 9 
 }
9 10 
 \arguments{
10 11 
 \item{count_data}{A SCE object}
Browse code

Moved example data to singlecellexperiment and misc_functions. This version of the toolkit won't work very well because I removed scater but some of the files haven't been converted yet. Follow the progress spreadsheet and test each function individually before merging to master

David Jenkins authored on 03/08/2017 22:34:14
Showing 1 changed files
man/plotTSNE.Rd
History View file @ 040d27f1
... ... 
@@ -2,9 +2,7 @@
2 2 
 % Please edit documentation in R/plotTSNE.R
3 3 
 \name{plotTSNE}
4 4 
 \alias{plotTSNE}
5 
-\title{Plot TSNE
6 
-
7 
-Use this function to plot PCA or tSNE results}
5 
+\title{Plot TSNE}
8 6 
 \usage{
9 7 
 plotTSNE(count_data, tsne_df = NULL, colorBy = NULL, shape = NULL)
10 8 
 }
... ... 
@@ -21,7 +19,5 @@ plotTSNE(count_data, tsne_df = NULL, colorBy = NULL, shape = NULL)
21 19 
 A TSNE plot
22 20 
 }
23 21 
 \description{
24 
-Plot TSNE
25 
-
26 22 
 Use this function to plot PCA or tSNE results
27 23 
 }
Browse code

Major overhall to Clustering Tab (w/ Sebastian)

Emma Briars authored on 26/04/2017 13:02:53
Showing 1 changed files
man/plotTSNE.Rd
History View file @ f4d70b88
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,27 @@
1 
+% Generated by roxygen2: do not edit by hand
2 
+% Please edit documentation in R/plotTSNE.R
3 
+\name{plotTSNE}
4 
+\alias{plotTSNE}
5 
+\title{Plot TSNE
6 
+
7 
+Use this function to plot PCA or tSNE results}
8 
+\usage{
9 
+plotTSNE(count_data, tsne_df = NULL, colorBy = NULL, shape = NULL)
10 
+}
11 
+\arguments{
12 
+\item{count_data}{A SCE object}
13 
+
14 
+\item{tsne_df}{tSNE data frame}
15 
+
16 
+\item{colorBy}{The variable to color clusters by}
17 
+
18 
+\item{shape}{Shape of the points}
19 
+}
20 
+\value{
21 
+A TSNE plot
22 
+}
23 
+\description{
24 
+Plot TSNE
25 
+
26 
+Use this function to plot PCA or tSNE results
27 
+}