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
)
Input SingleCellExperiment object with saved
dimension reduction components or a variable with saved results from
runPerCellQC
. Required.
Character vector or colData variable name. Indicates which
sample each cell belongs to. Default NULL
.
Groupings for each numeric value. Users 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 FALSE
.
Boolean. If TRUE
, will plot dots for each violin plot.
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
"median"
.
The text size of the summary statistic displayed
above the violin plot. Default 3
.
The base font size for all text. Default 15
.
Can be overwritten by titleSize
, axisSize
, and
axisLabelSize
.
Size of x/y-axis ticks. Default NULL
.
Size of x/y-axis labels. Default NULL
.
Transparency of the dots, values will be 0-1. Default 1
.
Removes grid in plot and sets axis title size to
10
when TRUE
. Default TRUE
.
Size of title of plot. Default NULL
.
Relative heights of plots when combine is set. Default
1
.
Relative widths of plots when combine is set. Default
1
.
Will label sample name in title of plot if TRUE
.
Default TRUE
.
Number of columns when plots are combined in a grid. Default
NULL
.
Number of rows when plots are combined in a grid. Default
NULL
.
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 <- runPerCellQC(sce)
#> Sat Mar 18 10:29:28 2023 ... Running 'perCellQCMetrics'
#> Sat Mar 18 10:29:28 2023 ...... Attempting to find mitochondrial genes by identifying features in 'rownames' that match mitochondrial genes from reference 'human' and ID type 'ensembl'.
plotRunPerCellQCResults(inSCE = sce)