A wrapper function which visualizes outputs from the runDoubletFinder function stored in the colData slot of the SingleCellExperiment object via various plots.
plotDoubletFinderResults( inSCE, sample = NULL, shape = NULL, groupBy = NULL, combinePlot = "all", violin = TRUE, boxplot = FALSE, dots = TRUE, reducedDimName = "UMAP", xlab = NULL, ylab = NULL, dim1 = NULL, dim2 = NULL, bin = NULL, binLabel = NULL, defaultTheme = TRUE, dotSize = 0.5, summary = "median", summaryTextSize = 3, transparency = 1, baseSize = 15, titleSize = NULL, axisLabelSize = NULL, axisSize = NULL, legendSize = NULL, legendTitleSize = NULL, relHeights = 1, relWidths = c(1, 1, 1), plotNCols = NULL, plotNRows = NULL, labelSamples = TRUE, samplePerColumn = TRUE, sampleRelHeights = 1, sampleRelWidths = 1 )
inSCE | Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runDoubletFinder. Required. |
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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 0.5. |
summary | Adds a summary statistic, as well as a crossbar to the violin plot. Options are "mean" or "median". Default NULL. |
summaryTextSize | The text size of the summary statistic displayed above the violin plot. Default 3. |
transparency | Transparency of the dots, values will be 0-1. Default 1. |
baseSize | The base font size for all text. Default 12. Can be overwritten by titleSize, axisSize, and axisLabelSize, legendSize, legendTitleSize. |
titleSize | Size of title of plot. Default NULL. |
axisLabelSize | Size of x/y-axis labels. Default NULL. |
axisSize | Size of x/y-axis ticks. Default NULL. |
legendSize | size of legend. Default NULL. |
legendTitleSize | size of legend title. Default NULL. |
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. |
labelSamples | Will label sample name in title of plot if TRUE. Default TRUE. |
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 <- runDoubletFinder(sce)#>#> Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric #> To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation' #> This message will be shown once per sessionplotDoubletFinderResults(inSCE=sce, reducedDimName="UMAP")