R/seuratFunctions.R
seuratJackStrawPlot.Rd
seuratJackStrawPlot Computes the plot object for jackstraw plot from the pca slot in the input sce object
seuratJackStrawPlot(
inSCE,
dims = NULL,
xmax = 0.1,
ymax = 0.3,
externalReduction = NULL
)
(sce) object from which to compute the jackstraw plot (pca should be computed)
Number of components to plot in Jackstraw. If NULL
, then
all components are plotted Default NULL
.
X-axis maximum on each QQ plot. Default 0.1
.
Y-axis maximum on each QQ plot. Default 0.3
.
Pass DimReduc object if PCA/ICA computed through
other libraries. Default NULL
.
plot object
data(scExample, package = "singleCellTK")
if (FALSE) {
sce <- seuratNormalizeData(sce, useAssay = "counts")
sce <- seuratFindHVG(sce, useAssay = "counts")
sce <- seuratScaleData(sce, useAssay = "counts")
sce <- seuratPCA(sce, useAssay = "counts")
sce <- seuratComputeJackStraw(sce, useAssay = "counts")
seuratJackStrawPlot(sce)
}