visualCNV: Clustering and plotting cells based on cnv score matrix using...

In CharleneZ95/infercnvPlus: Enhanced 'infercnv' package

Description

Clustering and plotting cells based on cnv score matrix using ComplexHeatmap package.

Args:

Usage

visualCNV(
  data,
  assay = NULL,
  ref_lab = "ref",
  obs_lab = "obs",
  distance_method = "euclidean",
  clustering_method = "ward.D2",
  cutree_k = NULL,
  colors = colorRampPalette(rev(brewer.pal(n = 11, name = "RdBu")))(11),
  border = TRUE,
  plot_dend = FALSE,
  out_file = "plot_cnv.png",
  out_path = "output_dir"
)

Arguments

data	an 'infercnv' object as produced by inferCNV.
assay	assay which assigned to use for plotting.
ref_lab	label for reference cells.
obs_lab	label for observations.
clustering_method	clustering method used. Accepts the same values as stats::hclust.
cutree_k	an integer scalar or vector with the desired number of groups.
colors	vector of colors used in heatmap.
border	whether draw border. The value can be logical or a string of color.
plot_dend	whether to plot dendrogram or not. The value should be logical.
out_file	filename to save plot.
out_path	output directory.
dist_method	distance measure used in clustering cells, possible values are 'correlation' for Pearson correlation and all the distances supported by stats::dist.

Value

Returns an 'infercnv' object including: 1. Clustering result. 2. Dendlist of 'cutree'.

CharleneZ95/infercnvPlus documentation built on April 9, 2020, 3:40 a.m.