A wrapper function which visualizes outputs from the
runEmptyDrops
function stored in the colData
slot of the
SingleCellExperiment object.
plotEmptyDropsResults(
inSCE,
sample = NULL,
combinePlot = "all",
fdrCutoff = 0.01,
defaultTheme = TRUE,
dotSize = 0.5,
titleSize = 18,
axisLabelSize = 18,
axisSize = 15,
legendSize = 15,
legendTitleSize = 16,
relHeights = 1,
relWidths = 1,
samplePerColumn = TRUE,
sampleRelHeights = 1,
sampleRelWidths = 1
)
Input SingleCellExperiment object with saved
dimension reduction components or a variable with saved results from
runEmptyDrops
. Required.
Character vector or colData variable name. Indicates which
sample each cell belongs to. Default NULL
.
Must be either "all"
, "sample"
, or object,
"none"
. "all"
will combine all plots into a single .ggplot
while "sample"
will output a list of plots separated by sample.
Default "all"
.
Numeric. Thresholds barcodes based on the FDR values from
runEmptyDrops
as "Empty Droplet" or "Putative Cell". Default
0.01
.
Removes grid in plot and sets axis title size to
10
when TRUE
. Default TRUE
.
Size of dots. Default 0.5
.
Size of title of plot. Default 18
.
Size of x/y-axis labels. Default 18
.
Size of x/y-axis ticks. Default 15
.
size of legend. Default 15
.
size of legend title. Default 16
.
Relative heights of plots when combine is set. Default
1
.
Relative widths of plots when combine is set. Default
1
.
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 <- runEmptyDrops(inSCE = sce)
#> Sat Mar 18 10:29:11 2023 ... Running 'emptyDrops'
plotEmptyDropsResults(inSCE = sce)
#> $scatterEmptyDrops
#>