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

Description Usage Arguments Value

View source: R/infercnvPlus.R

Description

Args:

Usage

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plotCNV(
  data,
  assay,
  ref_lab,
  obs_lab,
  dist_method,
  clustering_method,
  cutree_k,
  colors,
  border,
  plot_dend,
  out_file,
  out_path
)

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.

dist_method:

distance measure used in clustering cells, possible values are 'correlation' for Pearson correlation and all the distances supported by stats::dist.

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.

out_file:

filename to save plot

out_path:

output directory

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.