Joshua D. Campbell authored on 27/12/2022 18:45:08
| ... | ... |
@@ -105,12 +105,12 @@ expression value of the output corrected matrix from that of the original |
| 105 | 105 |
input matrix, and then devided by the input. |
| 106 | 106 |
} |
| 107 | 107 |
\examples{
|
| 108 |
-data(scExample, package = "singleCellTK") |
|
| 109 |
-sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'") |
|
| 110 | 108 |
\dontrun{
|
| 111 |
-# SoupX does not work for toy example, |
|
| 112 |
-# can be tested with `sce <- importExampleData("pbmc3k")`
|
|
| 109 |
+sce <- importExampleData("pbmc3k")
|
|
| 113 | 110 |
sce <- runSoupX(sce, sample = "sample") |
| 114 |
-plotSoupXResults(sce) |
|
| 111 |
+plotSoupXResults(sce, sample = "sample") |
|
| 115 | 112 |
} |
| 116 | 113 |
} |
| 114 |
+\seealso{
|
|
| 115 |
+runSoupX |
|
| 116 |
+} |
Yichen Wang authored on 11/08/2022 16:49:05
| ... | ... |
@@ -30,34 +30,34 @@ plotSoupXResults( |
| 30 | 30 |
) |
| 31 | 31 |
} |
| 32 | 32 |
\arguments{
|
| 33 |
-\item{inSCE}{A \linkS4class{SingleCellExperiment} object. With
|
|
| 33 |
+\item{inSCE}{A \linkS4class{SingleCellExperiment} object. With
|
|
| 34 | 34 |
\code{\link{runSoupX}} already applied.}
|
| 35 | 35 |
|
| 36 |
-\item{sample}{Character vector. Indicates which sample each cell belongs to.
|
|
| 36 |
+\item{sample}{Character vector. Indicates which sample each cell belongs to.
|
|
| 37 | 37 |
Default \code{NULL}.}
|
| 38 | 38 |
|
| 39 |
-\item{background}{Logical. Whether \code{background} was applied when
|
|
| 39 |
+\item{background}{Logical. Whether \code{background} was applied when
|
|
| 40 | 40 |
running \code{\link{runSoupX}}. Default \code{FALSE}.}
|
| 41 | 41 |
|
| 42 | 42 |
\item{reducedDimName}{Character. The embedding to use for plotting. Leave it
|
| 43 |
-\code{NULL} for using the sample-specific UMAPs generated when running
|
|
| 43 |
+\code{NULL} for using the sample-specific UMAPs generated when running
|
|
| 44 | 44 |
\code{\link{runSoupX}}. Default \code{NULL}.}
|
| 45 | 45 |
|
| 46 |
-\item{plotNCols}{Integer. Number of columns for the plot grid per sample.
|
|
| 47 |
-Will determine the number of top markers to show together with |
|
| 46 |
+\item{plotNCols}{Integer. Number of columns for the plot grid per sample.
|
|
| 47 |
+Will determine the number of top markers to show together with |
|
| 48 | 48 |
\code{plotNRows}. Default \code{3}.}
|
| 49 | 49 |
|
| 50 | 50 |
\item{plotNRows}{Integer. Number of rows for the plot grid per sample. Will
|
| 51 | 51 |
determine the number of top markers to show together with \code{plotNCols}.
|
| 52 | 52 |
Default \code{2}.}
|
| 53 | 53 |
|
| 54 |
-\item{baseSize}{Numeric. The base font size for all text. Default 12. Can be
|
|
| 55 |
-overwritten by titleSize, axisSize, and axisLabelSize, legendSize, |
|
| 54 |
+\item{baseSize}{Numeric. The base font size for all text. Default 12. Can be
|
|
| 55 |
+overwritten by titleSize, axisSize, and axisLabelSize, legendSize, |
|
| 56 | 56 |
legendTitleSize. Default \code{8}.}
|
| 57 | 57 |
|
| 58 |
-\item{combinePlot}{Must be either \code{"all"}, \code{"sample"}, or
|
|
| 59 |
-\code{"none"}. \code{"all"} will combine all plots into a single
|
|
| 60 |
-\code{.ggplot} object, while \code{"sample"} will output a list of plots
|
|
| 58 |
+\item{combinePlot}{Must be either \code{"all"}, \code{"sample"}, or
|
|
| 59 |
+\code{"none"}. \code{"all"} will combine all plots into a single
|
|
| 60 |
+\code{.ggplot} object, while \code{"sample"} will output a list of plots
|
|
| 61 | 61 |
separated by sample. Default \code{"all"}.}
|
| 62 | 62 |
|
| 63 | 63 |
\item{xlab}{Character vector. Label for x-axis. Default \code{NULL}.}
|
| ... | ... |
@@ -71,10 +71,10 @@ separated by sample. Default \code{"all"}.}
|
| 71 | 71 |
\item{labelClusters}{Logical. Whether the cluster labels are plotted. Default
|
| 72 | 72 |
\code{FALSE}.}
|
| 73 | 73 |
|
| 74 |
-\item{clusterLabelSize}{Numeric. Determines the size of cluster label when
|
|
| 74 |
+\item{clusterLabelSize}{Numeric. Determines the size of cluster label when
|
|
| 75 | 75 |
\code{labelClusters} is set to \code{TRUE}. Default \code{3.5}.}
|
| 76 | 76 |
|
| 77 |
-\item{defaultTheme}{Logical. Adds grid to plot when \code{TRUE}. Default
|
|
| 77 |
+\item{defaultTheme}{Logical. Adds grid to plot when \code{TRUE}. Default
|
|
| 78 | 78 |
\code{TRUE}.}
|
| 79 | 79 |
|
| 80 | 80 |
\item{dotSize}{Numeric. Size of dots. Default \code{0.5}.}
|
| ... | ... |
@@ -96,19 +96,19 @@ to 1. Default \code{1}.}
|
| 96 | 96 |
ggplot object of the combination of UMAPs. See description. |
| 97 | 97 |
} |
| 98 | 98 |
\description{
|
| 99 |
-This function will generate a combination of plots basing on the |
|
| 100 |
-correction done by SoupX. For each sample, there will be a UMAP with cluster |
|
| 101 |
-labeling, followed by a number of UMAPs showing the change in selected top |
|
| 102 |
-markers. The cluster labeling is what should be used for SoupX to estimate |
|
| 103 |
-the contamination. The Soup Fraction is calculated by subtracting the gene |
|
| 104 |
-expression value of the output corrected matrix from that of the original |
|
| 99 |
+This function will generate a combination of plots basing on the |
|
| 100 |
+correction done by SoupX. For each sample, there will be a UMAP with cluster |
|
| 101 |
+labeling, followed by a number of UMAPs showing the change in selected top |
|
| 102 |
+markers. The cluster labeling is what should be used for SoupX to estimate |
|
| 103 |
+the contamination. The Soup Fraction is calculated by subtracting the gene |
|
| 104 |
+expression value of the output corrected matrix from that of the original |
|
| 105 | 105 |
input matrix, and then devided by the input. |
| 106 | 106 |
} |
| 107 | 107 |
\examples{
|
| 108 | 108 |
data(scExample, package = "singleCellTK") |
| 109 | 109 |
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'") |
| 110 | 110 |
\dontrun{
|
| 111 |
-# SoupX does not work for toy example, |
|
| 111 |
+# SoupX does not work for toy example, |
|
| 112 | 112 |
# can be tested with `sce <- importExampleData("pbmc3k")`
|
| 113 | 113 |
sce <- runSoupX(sce, sample = "sample") |
| 114 | 114 |
plotSoupXResults(sce) |
Yichen Wang authored on 03/03/2022 05:34:46
| 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,116 @@ |
| 1 |
+% Generated by roxygen2: do not edit by hand |
|
| 2 |
+% Please edit documentation in R/runSoupX.R |
|
| 3 |
+\name{plotSoupXResults}
|
|
| 4 |
+\alias{plotSoupXResults}
|
|
| 5 |
+\title{Plot SoupX Result}
|
|
| 6 |
+\usage{
|
|
| 7 |
+plotSoupXResults( |
|
| 8 |
+ inSCE, |
|
| 9 |
+ sample = NULL, |
|
| 10 |
+ background = FALSE, |
|
| 11 |
+ reducedDimName = NULL, |
|
| 12 |
+ plotNCols = 3, |
|
| 13 |
+ plotNRows = 2, |
|
| 14 |
+ baseSize = 8, |
|
| 15 |
+ combinePlot = c("all", "sample", "none"),
|
|
| 16 |
+ xlab = NULL, |
|
| 17 |
+ ylab = NULL, |
|
| 18 |
+ dim1 = NULL, |
|
| 19 |
+ dim2 = NULL, |
|
| 20 |
+ labelClusters = FALSE, |
|
| 21 |
+ clusterLabelSize = 3.5, |
|
| 22 |
+ defaultTheme = TRUE, |
|
| 23 |
+ dotSize = 0.5, |
|
| 24 |
+ transparency = 1, |
|
| 25 |
+ titleSize = NULL, |
|
| 26 |
+ axisLabelSize = NULL, |
|
| 27 |
+ axisSize = NULL, |
|
| 28 |
+ legendSize = NULL, |
|
| 29 |
+ legendTitleSize = NULL |
|
| 30 |
+) |
|
| 31 |
+} |
|
| 32 |
+\arguments{
|
|
| 33 |
+\item{inSCE}{A \linkS4class{SingleCellExperiment} object. With
|
|
| 34 |
+\code{\link{runSoupX}} already applied.}
|
|
| 35 |
+ |
|
| 36 |
+\item{sample}{Character vector. Indicates which sample each cell belongs to.
|
|
| 37 |
+Default \code{NULL}.}
|
|
| 38 |
+ |
|
| 39 |
+\item{background}{Logical. Whether \code{background} was applied when
|
|
| 40 |
+running \code{\link{runSoupX}}. Default \code{FALSE}.}
|
|
| 41 |
+ |
|
| 42 |
+\item{reducedDimName}{Character. The embedding to use for plotting. Leave it
|
|
| 43 |
+\code{NULL} for using the sample-specific UMAPs generated when running
|
|
| 44 |
+\code{\link{runSoupX}}. Default \code{NULL}.}
|
|
| 45 |
+ |
|
| 46 |
+\item{plotNCols}{Integer. Number of columns for the plot grid per sample.
|
|
| 47 |
+Will determine the number of top markers to show together with |
|
| 48 |
+\code{plotNRows}. Default \code{3}.}
|
|
| 49 |
+ |
|
| 50 |
+\item{plotNRows}{Integer. Number of rows for the plot grid per sample. Will
|
|
| 51 |
+determine the number of top markers to show together with \code{plotNCols}.
|
|
| 52 |
+Default \code{2}.}
|
|
| 53 |
+ |
|
| 54 |
+\item{baseSize}{Numeric. The base font size for all text. Default 12. Can be
|
|
| 55 |
+overwritten by titleSize, axisSize, and axisLabelSize, legendSize, |
|
| 56 |
+legendTitleSize. Default \code{8}.}
|
|
| 57 |
+ |
|
| 58 |
+\item{combinePlot}{Must be either \code{"all"}, \code{"sample"}, or
|
|
| 59 |
+\code{"none"}. \code{"all"} will combine all plots into a single
|
|
| 60 |
+\code{.ggplot} object, while \code{"sample"} will output a list of plots
|
|
| 61 |
+separated by sample. Default \code{"all"}.}
|
|
| 62 |
+ |
|
| 63 |
+\item{xlab}{Character vector. Label for x-axis. Default \code{NULL}.}
|
|
| 64 |
+ |
|
| 65 |
+\item{ylab}{Character vector. Label for y-axis. Default \code{NULL}.}
|
|
| 66 |
+ |
|
| 67 |
+\item{dim1}{See \code{\link{plotSCEDimReduceColData}}. Default \code{NULL}.}
|
|
| 68 |
+ |
|
| 69 |
+\item{dim2}{See \code{\link{plotSCEDimReduceColData}}. Default \code{NULL}.}
|
|
| 70 |
+ |
|
| 71 |
+\item{labelClusters}{Logical. Whether the cluster labels are plotted. Default
|
|
| 72 |
+\code{FALSE}.}
|
|
| 73 |
+ |
|
| 74 |
+\item{clusterLabelSize}{Numeric. Determines the size of cluster label when
|
|
| 75 |
+\code{labelClusters} is set to \code{TRUE}. Default \code{3.5}.}
|
|
| 76 |
+ |
|
| 77 |
+\item{defaultTheme}{Logical. Adds grid to plot when \code{TRUE}. Default
|
|
| 78 |
+\code{TRUE}.}
|
|
| 79 |
+ |
|
| 80 |
+\item{dotSize}{Numeric. Size of dots. Default \code{0.5}.}
|
|
| 81 |
+ |
|
| 82 |
+\item{transparency}{Numeric. Transparency of the dots, values will be from 0
|
|
| 83 |
+to 1. Default \code{1}.}
|
|
| 84 |
+ |
|
| 85 |
+\item{titleSize}{Numeric. Size of title of plot. Default \code{15}.}
|
|
| 86 |
+ |
|
| 87 |
+\item{axisLabelSize}{Numeric. Size of x/y-axis labels. Default \code{NULL}.}
|
|
| 88 |
+ |
|
| 89 |
+\item{axisSize}{Numeric. Size of x/y-axis ticks. Default \code{NULL}.}
|
|
| 90 |
+ |
|
| 91 |
+\item{legendSize}{Numeric. Size of legend. Default \code{NULL}.}
|
|
| 92 |
+ |
|
| 93 |
+\item{legendTitleSize}{Numeric. Size of legend title. Default \code{NULL}.}
|
|
| 94 |
+} |
|
| 95 |
+\value{
|
|
| 96 |
+ggplot object of the combination of UMAPs. See description. |
|
| 97 |
+} |
|
| 98 |
+\description{
|
|
| 99 |
+This function will generate a combination of plots basing on the |
|
| 100 |
+correction done by SoupX. For each sample, there will be a UMAP with cluster |
|
| 101 |
+labeling, followed by a number of UMAPs showing the change in selected top |
|
| 102 |
+markers. The cluster labeling is what should be used for SoupX to estimate |
|
| 103 |
+the contamination. The Soup Fraction is calculated by subtracting the gene |
|
| 104 |
+expression value of the output corrected matrix from that of the original |
|
| 105 |
+input matrix, and then devided by the input. |
|
| 106 |
+} |
|
| 107 |
+\examples{
|
|
| 108 |
+data(scExample, package = "singleCellTK") |
|
| 109 |
+sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'") |
|
| 110 |
+\dontrun{
|
|
| 111 |
+# SoupX does not work for toy example, |
|
| 112 |
+# can be tested with `sce <- importExampleData("pbmc3k")`
|
|
| 113 |
+sce <- runSoupX(sce, sample = "sample") |
|
| 114 |
+plotSoupXResults(sce) |
|
| 115 |
+} |
|
| 116 |
+} |