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 )
inSCE | (sce) object from which to compute the jackstraw plot (pca should be computed) |
---|---|
dims | Number of components to plot in Jackstraw. If |
xmax | X-axis maximum on each QQ plot. Default |
ymax | Y-axis maximum on each QQ plot. Default |
externalReduction | Pass DimReduc object if PCA/ICA computed through
other libraries. Default |
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) }