plotScdsHybridResults: Plots for runCxdsBcdsHybrid outputs.

Description Usage Arguments Value Examples

View source: R/ggPerQCWrapper.R

Description

A wrapper function which visualizes outputs from the runCxdsBcdsHybrid function stored in the colData slot of the SingleCellExperiment object via various plots.

Usage

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plotScdsHybridResults(
  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
)

Arguments

inSCE

Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runCxdsBcdsHybrid. 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.

Value

list of .ggplot objects

Examples

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data(scExample, package="singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- getUMAP(inSCE=sce, useAssay="counts", reducedDimName="UMAP")
sce <- runCxdsBcdsHybrid(sce)
plotScdsHybridResults(inSCE=sce, reducedDimName="UMAP")

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.