Create_NGCHM: Create Next Generation Clustered Heat Map (NG-CHM)

In broadinstitute/infercnvNGCHM: InferCNV Interface To Use Next Generation Clustered Heat Maps (NGCHM)

Description

Create highly interactive heat maps for single cell expression data using Next Generation Clustered Heat Map (NG-CHM). NG-CHM was developed and maintained by MD Anderson Department of Bioinformatics and Computational Biology in collaboration with In Silico Solutions.

Usage

Create_NGCHM(infercnv_obj, path_to_shaidyMapGen, out_dir, title = NULL,
  gene_symbol = NULL, x.center = NA, x.range = NA)

Arguments

infercnv_obj	(S4) InferCNV S4 object holding expression data, gene location data, annotation information.
path_to_shaidyMapGen	(string) Path to the java application ShaidyMapGen.jar
out_dir	(string) Path to where the infercnv.ngchm output file should be saved to
title	(string) Title that will be used for the heatmap
gene_symbol	(string) Specify the label type that is given to the gene needed to create linkouts, default is NULL
x.center	(integer) Center expression value for heatmap coloring.
x.range	(integer) Values for minimum and maximum thresholds for heatmap coloring.

Value

a NGCHM file named infercnv.ngchm and saves it to the output directory given to infercnv.

broadinstitute/infercnvNGCHM documentation built on July 21, 2021, 11:49 a.m.