plotBcdsResults {singleCellTK} | R Documentation |
A wrapper function which visualizes outputs from the runBcds function stored in the colData slot of the SingleCellExperiment object via various plots.
plotBcdsResults( inSCE, sample = NULL, shape = NULL, groupBy = NULL, combinePlot = "all", violin = TRUE, boxplot = FALSE, dots = TRUE, reducedDimName = NULL, xlab = NULL, ylab = NULL, dim1 = NULL, dim2 = NULL, bin = NULL, binLabel = NULL, defaultTheme = TRUE, dotSize = 1, transparency = 1, titleSize = 18, axisLabelSize = 18, axisSize = 15, legendSize = 15, legendTitleSize = 16, relHeights = c(1.5, 1, 1), relWidths = c(1, 1, 1), plotNCols = NULL, plotNRows = NULL, plotLabels = "default", plotLabelSize = 20, plotLabelPositionX = NULL, plotLabelPositionY = NULL, samplePerColumn = TRUE, sampleRelHeights = 1, sampleRelWidths = 1 )
inSCE |
Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runBcds. Required. |
sample |
Character vector. Indicates which sample each cell belongs to. Default NULL. |
shape |
If provided, add shapes based on the value. |
groupBy |
Groupings for each numeric value. A user may input a vector equal length to the number of the samples in the SingleCellExperiment object, or can be retrieved from the colData slot. Default NULL. |
combinePlot |
Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object, while "sample" will output a list of plots separated by sample. Default "all". |
violin |
Boolean. If TRUE, will plot the violin plot. Default TRUE. |
boxplot |
Boolean. If TRUE, will plot boxplots for each violin plot. Default TRUE. |
dots |
Boolean. If TRUE, will plot dots for each violin plot. Default TRUE. |
reducedDimName |
Saved dimension reduction name in the SingleCellExperiment object. Required. |
xlab |
Character vector. Label for x-axis. Default NULL. |
ylab |
Character vector. Label for y-axis. Default NULL. |
dim1 |
1st dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL. |
dim2 |
2nd dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL. |
bin |
Numeric vector. If single value, will divide the numeric values into the 'bin' groups. If more than one value, will bin numeric values using values as a cut point. |
binLabel |
Character vector. Labels for the bins created by the 'bin' parameter. Default NULL. |
defaultTheme |
Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE. |
dotSize |
Size of dots. Default 1. |
transparency |
Transparency of the dots, values will be 0-1. Default 1. |
titleSize |
Size of title of plot. Default 18. |
axisLabelSize |
Size of x/y-axis labels. Default 18. |
axisSize |
Size of x/y-axis ticks. Default 15. |
legendSize |
size of legend. Default 15. |
legendTitleSize |
size of legend title. Default 16. |
relHeights |
Relative heights of plots when combine is set. |
relWidths |
Relative widths of plots when combine is set. |
plotNCols |
Number of columns when plots are combined in a grid. |
plotNRows |
Number of rows when plots are combined in a grid. |
plotLabels |
labels to each plot. If set to "default", will use the name of the samples as the labels. If set to "none", no label will be plotted. |
plotLabelSize |
size of labels |
plotLabelPositionX |
Numeric vector. The X position of the plot label. |
plotLabelPositionY |
Numeric vector. The Y position of the plot label. |
samplePerColumn |
If TRUE, when there are multiple samples and combining by "all", the output .ggplot will have plots from each sample on a single column. Default TRUE. |
sampleRelHeights |
If there are multiple samples and combining by "all", the relative heights for each plot. |
sampleRelWidths |
If there are multiple samples and combining by "all", the relative widths for each plot. |
list of .ggplot objects
data(scExample, package="singleCellTK") sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'") sce <- getUMAP(inSCE=sce, useAssay="counts", reducedDimName="UMAP") sce <- runBcds(sce) plotBcdsResults(inSCE=sce, reducedDimName="UMAP")