A wrapper function which visualizes outputs from the
runScDblFinder
function stored in the colData slot of the
SingleCellExperiment object via various plots.
plotScDblFinderResults(
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
)
Input SingleCellExperiment object with saved
dimension reduction components or a variable with saved results from
runScDblFinder
. Required.
Character vector or colData variable name. Indicates which
sample each cell belongs to. Default NULL
.
If provided, add shapes based on the value. Default NULL
.
Groupings for each numeric value. A user may input a vector
equal length to the number of the samples in inSCE
, or can be
retrieved from the colData slot. Default NULL
.
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"
.
Boolean. If TRUE
, will plot the violin plot. Default
TRUE
.
Boolean. If TRUE
, will plot boxplots for each violin
plot. Default TRUE
.
Boolean. If TRUE
, will plot dots for each violin plot.
Default TRUE
.
Saved dimension reduction name in inSCE
.
Default "UMAP"
.
Character vector. Label for x-axis. Default NULL
.
Character vector. Label for y-axis. Default NULL
.
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
.
2nd dimension to be used for plotting. Similar to dim1
.
Default is NULL
.
Numeric vector. If single value, will divide the numeric values
into bin
groups. If more than one value, will bin numeric values using
values as a cut point. Default NULL
.
Character vector. Labels for the bins created by bin
.
Default NULL
.
Removes grid in plot and sets axis title size to
10
when TRUE
. Default TRUE
.
Size of dots. Default 0.5
.
Adds a summary statistic, as well as a crossbar to the
violin plot. Options are "mean"
or "median"
. Default
NULL
.
The text size of the summary statistic displayed
above the violin plot. Default 3
.
Transparency of the dots, values will be 0-1. Default
1
.
The base font size for all text. Default 12
.
Can be overwritten by titleSize
, axisSize
, and
axisLabelSize
, legendSize
, legendTitleSize
.
Size of title of plot. Default NULL
.
Size of x/y-axis labels. Default NULL
.
Size of x/y-axis ticks. Default NULL
.
size of legend. Default NULL
.
size of legend title. Default NULL
.
Relative heights of plots when combine is set. Default 1
.
Relative widths of plots when combine is set. Default
c(1, 1, 1)
.
Number of columns when plots are combined in a grid. Default
NULL
.
Number of rows when plots are combined in a grid. Default
NULL
.
Will label sample name in title of plot if TRUE. Default
TRUE
.
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
.
If there are multiple samples and combining by
"all"
, the relative heights for each plot. Default 1
.
If there are multiple samples and combining by
"all"
, the relative widths for each plot. Default 1
.
list of .ggplot objects
data(scExample, package="singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- runQuickUMAP(sce)
#> Sat Mar 18 10:29:38 2023 ... Computing Scater UMAP for sample 'pbmc_4k'.
#> Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
#> Also defined by ‘spam’
#> Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
#> Also defined by ‘spam’
#> Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
#> Also defined by ‘spam’
sce <- runScDblFinder(sce)
#> Sat Mar 18 10:29:41 2023 ... Running 'scDblFinder'
plotScDblFinderResults(inSCE = sce, reducedDimName = "UMAP")