Josh Campbell authored on 15/04/2024 19:20:47
| ... | ... |
@@ -57,7 +57,8 @@ be performed prior to using this function |
| 57 | 57 |
data("sceBatches")
|
| 58 | 58 |
logcounts(sceBatches) <- log1p(counts(sceBatches)) |
| 59 | 59 |
sce.w <- subsetSCECols(sceBatches, colData = "batch == 'w'") |
| 60 |
-sce.w <- runWilcox(sce.w, class = "cell_type", classGroup1 = "alpha", |
|
| 60 |
+sce.w <- runWilcox(sce.w, class = "cell_type", |
|
| 61 |
+ classGroup1 = "alpha", classGroup2 = "beta", |
|
| 61 | 62 |
groupName1 = "w.alpha", groupName2 = "w.beta", |
| 62 | 63 |
analysisName = "w.aVSb") |
| 63 | 64 |
plotDEGViolin(sce.w, "w.aVSb") |
Yichen Wang authored on 11/08/2022 20:00:51
| ... | ... |
@@ -55,7 +55,7 @@ be performed prior to using this function |
| 55 | 55 |
} |
| 56 | 56 |
\examples{
|
| 57 | 57 |
data("sceBatches")
|
| 58 |
-logcounts(sceBatches) <- log(counts(sceBatches) + 1) |
|
| 58 |
+logcounts(sceBatches) <- log1p(counts(sceBatches)) |
|
| 59 | 59 |
sce.w <- subsetSCECols(sceBatches, colData = "batch == 'w'") |
| 60 | 60 |
sce.w <- runWilcox(sce.w, class = "cell_type", classGroup1 = "alpha", |
| 61 | 61 |
groupName1 = "w.alpha", groupName2 = "w.beta", |
Yichen Wang authored on 29/06/2022 23:30:51
| ... | ... |
@@ -50,7 +50,7 @@ A ggplot object of violin plot |
| 50 | 50 |
Generate violin plot to show the expression of top DEGs |
| 51 | 51 |
} |
| 52 | 52 |
\details{
|
| 53 |
-Any of the differential expression analysis method from SCTK should |
|
| 53 |
+Any of the differential expression analysis method from SCTK should |
|
| 54 | 54 |
be performed prior to using this function |
| 55 | 55 |
} |
| 56 | 56 |
\examples{
|
Yichen Wang authored on 23/11/2021 03:25:28
| ... | ... |
@@ -2,8 +2,7 @@ |
| 2 | 2 |
% Please edit documentation in R/plotDEAnalysis.R |
| 3 | 3 |
\name{plotDEGViolin}
|
| 4 | 4 |
\alias{plotDEGViolin}
|
| 5 |
-\title{plot the violin plot to show visualize the expression distribution of DEGs
|
|
| 6 |
-identified by differential expression analysis} |
|
| 5 |
+\title{Generate violin plot to show the expression of top DEGs}
|
|
| 7 | 6 |
\usage{
|
| 8 | 7 |
plotDEGViolin( |
| 9 | 8 |
inSCE, |
| ... | ... |
@@ -18,8 +17,7 @@ plotDEGViolin( |
| 18 | 17 |
) |
| 19 | 18 |
} |
| 20 | 19 |
\arguments{
|
| 21 |
-\item{inSCE}{\linkS4class{SingleCellExperiment} inherited object.
|
|
| 22 |
-\code{runMAST()} has to be run in advance.}
|
|
| 20 |
+\item{inSCE}{\linkS4class{SingleCellExperiment} inherited object.}
|
|
| 23 | 21 |
|
| 24 | 22 |
\item{useResult}{character. A string specifying the \code{analysisName}
|
| 25 | 23 |
used when running a differential expression analysis function.} |
| ... | ... |
@@ -49,8 +47,11 @@ to see if the counts are logged. Default \code{TRUE}}
|
| 49 | 47 |
A ggplot object of violin plot |
| 50 | 48 |
} |
| 51 | 49 |
\description{
|
| 52 |
-plot the violin plot to show visualize the expression distribution of DEGs |
|
| 53 |
-identified by differential expression analysis |
|
| 50 |
+Generate violin plot to show the expression of top DEGs |
|
| 51 |
+} |
|
| 52 |
+\details{
|
|
| 53 |
+Any of the differential expression analysis method from SCTK should |
|
| 54 |
+be performed prior to using this function |
|
| 54 | 55 |
} |
| 55 | 56 |
\examples{
|
| 56 | 57 |
data("sceBatches")
|
Yichen Wang authored on 10/05/2021 22:58:10
| ... | ... |
@@ -52,3 +52,12 @@ A ggplot object of violin plot |
| 52 | 52 |
plot the violin plot to show visualize the expression distribution of DEGs |
| 53 | 53 |
identified by differential expression analysis |
| 54 | 54 |
} |
| 55 |
+\examples{
|
|
| 56 |
+data("sceBatches")
|
|
| 57 |
+logcounts(sceBatches) <- log(counts(sceBatches) + 1) |
|
| 58 |
+sce.w <- subsetSCECols(sceBatches, colData = "batch == 'w'") |
|
| 59 |
+sce.w <- runWilcox(sce.w, class = "cell_type", classGroup1 = "alpha", |
|
| 60 |
+ groupName1 = "w.alpha", groupName2 = "w.beta", |
|
| 61 |
+ analysisName = "w.aVSb") |
|
| 62 |
+plotDEGViolin(sce.w, "w.aVSb") |
|
| 63 |
+} |
Yichen Wang authored on 19/10/2020 15:42:20
| ... | ... |
@@ -13,6 +13,7 @@ plotDEGViolin( |
| 13 | 13 |
nrow = 6, |
| 14 | 14 |
ncol = 6, |
| 15 | 15 |
defaultTheme = TRUE, |
| 16 |
+ isLogged = TRUE, |
|
| 16 | 17 |
check_sanity = TRUE |
| 17 | 18 |
) |
| 18 | 19 |
} |
| ... | ... |
@@ -37,6 +38,10 @@ where to search for the labeling text. Default \code{NULL}.}
|
| 37 | 38 |
\item{defaultTheme}{Logical scalar. Whether to use default SCTK theme in
|
| 38 | 39 |
ggplot. Default \code{TRUE}.}
|
| 39 | 40 |
|
| 41 |
+\item{isLogged}{Logical scalar. Whether the assay used for the analysis is
|
|
| 42 |
+logged. If not, will do a \code{log(assay + 1)} transformation. Default
|
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| 43 |
+\code{TRUE}.}
|
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+ |
|
| 40 | 45 |
\item{check_sanity}{Logical scalar. Whether to perform MAST's sanity check
|
| 41 | 46 |
to see if the counts are logged. Default \code{TRUE}}
|
| 42 | 47 |
} |
Yichen Wang authored on 15/10/2020 16:46:08
| ... | ... |
@@ -12,7 +12,8 @@ plotDEGViolin( |
| 12 | 12 |
labelBy = NULL, |
| 13 | 13 |
nrow = 6, |
| 14 | 14 |
ncol = 6, |
| 15 |
- defaultTheme = TRUE |
|
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+ defaultTheme = TRUE, |
|
| 16 |
+ check_sanity = TRUE |
|
| 16 | 17 |
) |
| 17 | 18 |
} |
| 18 | 19 |
\arguments{
|
| ... | ... |
@@ -35,6 +36,9 @@ where to search for the labeling text. Default \code{NULL}.}
|
| 35 | 36 |
|
| 36 | 37 |
\item{defaultTheme}{Logical scalar. Whether to use default SCTK theme in
|
| 37 | 38 |
ggplot. Default \code{TRUE}.}
|
| 39 |
+ |
|
| 40 |
+\item{check_sanity}{Logical scalar. Whether to perform MAST's sanity check
|
|
| 41 |
+to see if the counts are logged. Default \code{TRUE}}
|
|
| 38 | 42 |
} |
| 39 | 43 |
\value{
|
| 40 | 44 |
A ggplot object of violin plot |
Yichen Wang authored on 18/06/2020 01:48:20
| 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,45 @@ |
| 1 |
+% Generated by roxygen2: do not edit by hand |
|
| 2 |
+% Please edit documentation in R/plotDEAnalysis.R |
|
| 3 |
+\name{plotDEGViolin}
|
|
| 4 |
+\alias{plotDEGViolin}
|
|
| 5 |
+\title{plot the violin plot to show visualize the expression distribution of DEGs
|
|
| 6 |
+identified by differential expression analysis} |
|
| 7 |
+\usage{
|
|
| 8 |
+plotDEGViolin( |
|
| 9 |
+ inSCE, |
|
| 10 |
+ useResult, |
|
| 11 |
+ threshP = FALSE, |
|
| 12 |
+ labelBy = NULL, |
|
| 13 |
+ nrow = 6, |
|
| 14 |
+ ncol = 6, |
|
| 15 |
+ defaultTheme = TRUE |
|
| 16 |
+) |
|
| 17 |
+} |
|
| 18 |
+\arguments{
|
|
| 19 |
+\item{inSCE}{\linkS4class{SingleCellExperiment} inherited object.
|
|
| 20 |
+\code{runMAST()} has to be run in advance.}
|
|
| 21 |
+ |
|
| 22 |
+\item{useResult}{character. A string specifying the \code{analysisName}
|
|
| 23 |
+used when running a differential expression analysis function.} |
|
| 24 |
+ |
|
| 25 |
+\item{threshP}{logical. Whether to plot threshold values from adaptive
|
|
| 26 |
+thresholding, instead of using the assay used by \code{runMAST()}. Default
|
|
| 27 |
+\code{FALSE}.}
|
|
| 28 |
+ |
|
| 29 |
+\item{labelBy}{A single character for a column of \code{rowData(inSCE)} as
|
|
| 30 |
+where to search for the labeling text. Default \code{NULL}.}
|
|
| 31 |
+ |
|
| 32 |
+\item{nrow}{Integer. Number of rows in the plot grid. Default \code{6}.}
|
|
| 33 |
+ |
|
| 34 |
+\item{ncol}{Integer. Number of columns in the plot grid. Default \code{6}.}
|
|
| 35 |
+ |
|
| 36 |
+\item{defaultTheme}{Logical scalar. Whether to use default SCTK theme in
|
|
| 37 |
+ggplot. Default \code{TRUE}.}
|
|
| 38 |
+} |
|
| 39 |
+\value{
|
|
| 40 |
+A ggplot object of violin plot |
|
| 41 |
+} |
|
| 42 |
+\description{
|
|
| 43 |
+plot the violin plot to show visualize the expression distribution of DEGs |
|
| 44 |
+identified by differential expression analysis |
|
| 45 |
+} |