A wrapper function which visualizes outputs from the runPerCellQC function stored in the colData slot of the SingleCellExperiment object via various plots.
plotRunPerCellQCResults( inSCE, sample = NULL, groupBy = NULL, combinePlot = "all", violin = TRUE, boxplot = FALSE, dots = TRUE, dotSize = 0.5, summary = "median", summaryTextSize = 3, baseSize = 15, axisSize = NULL, axisLabelSize = NULL, transparency = 1, defaultTheme = TRUE, titleSize = NULL, relHeights = 1, relWidths = 1, labelSamples = TRUE, plotNCols = NULL, plotNRows = NULL, samplePerColumn = TRUE, sampleRelHeights = 1, sampleRelWidths = 1 )
inSCE | Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runPerCellQC. Required. |
---|---|
sample | Character vector. Indicates which sample each cell belongs to. Default NULL. |
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 FALSE. |
dots | Boolean. If TRUE, will plot dots for each violin plot. 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 "median". |
summaryTextSize | The text size of the summary statistic displayed above the violin plot. Default 3. |
baseSize | The base font size for all text. Default 15. Can be overwritten by titleSize, axisSize, and axisLabelSize. |
axisSize | Size of x/y-axis ticks. Default NULL. |
axisLabelSize | Size of x/y-axis labels. Default NULL. |
transparency | Transparency of the dots, values will be 0-1. Default 1. |
defaultTheme | Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE. |
titleSize | Size of title of plot. Default NULL. |
relHeights | Relative heights of plots when combine is set. |
relWidths | Relative widths of plots when combine is set. |
labelSamples | Will label sample name in title of plot if TRUE. Default TRUE. |
plotNCols | Number of columns when plots are combined in a grid. |
plotNRows | Number of rows when plots are combined in a grid. |
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") if (FALSE) { sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'") sce <- runPerCellQC(sce) plotRunPerCellQCResults(inSCE=sce) }