Seurat (version 2.3.4)

MetageneBicorPlot: Plot CC bicor saturation plot

Description

The function provides a useful plot for evaluating the number of CCs to proceed with in the Seurat alignment workflow. Here we look at the biweight midcorrelation (bicor) of the Xth gene ranked by minimum bicor across the specified CCs for each group in the grouping.var. For alignment of more than two groups, we average the bicor results for the reference group across the pairwise alignments.

Usage

MetageneBicorPlot(object, bicor.data, grouping.var, dims.eval, gene.num = 30,
  num.possible.genes = 2000, return.mat = FALSE, smooth = TRUE,
  display.progress = TRUE)

Arguments

object

A Seurat object

bicor.data

Optionally provide data.frame returned by function to avoid recalculation

grouping.var

Grouping variable specified in alignment procedure

dims.eval

dimensions to evalutate the bicor for

gene.num

Xth gene to look at bicor for

num.possible.genes

Number of possible genes to search when choosing genes for the metagene. Set to 2000 by default. Lowering will decrease runtime but may result in metagenes constructed on fewer than num.genes genes.

return.mat

Return data.matrix instead of ggplot2 object

smooth

Smooth curves

display.progress

Show progress bar

Examples

# NOT RUN {
pbmc_small <- DoKMeans(object = pbmc_small, k.genes = 3)
KMeansHeatmap(object = pbmc_small)

# }