Calculate and produce a list of thresholded counts (on natural scale),
thresholds, bins, densities estimated on each bin, and the original data from
thresholdSCRNACountMatrix
plotMASTThresholdGenes(
inSCE,
useAssay = "logcounts",
doPlot = TRUE,
isLogged = TRUE,
check_sanity = TRUE
)
SingleCellExperiment object
character, default "logcounts"
Logical scalar. Whether to directly plot in the plotting area.
If FALSE
, will return a graphical object which can be visualized with
grid.draw()
. Default TRUE
.
Logical scalar. Whether the assay used for the analysis is
logged. If not, will do a log(assay + 1)
transformation. Default
TRUE
.
Logical scalar. Whether to perform MAST's sanity check
to see if the counts are logged. Default TRUE
Plot the thresholding onto the plotting region if plot == TRUE
or a graphical object if plot == FALSE
.
data("mouseBrainSubsetSCE")
plotMASTThresholdGenes(mouseBrainSubsetSCE)
#> `fData` has no primerid. I'll make something up.
#> `cData` has no wellKey. I'll make something up.
#> Assuming data assay in position 1, with name et is log-transformed.
#> Warning: calling par(new=TRUE) with no plot