hfc: hfc, heatmap for clustering

In kendomaniac/rCASC: rCASC reproducible Classification Analysis of Single Cell Sequencing Data

hfc, heatmap for clustering

Description

This function generate heatmap and other plot based on clustering and on a specific gene list

Usage

hfc(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  nCluster,
  separator,
  lfn,
  geneNameControl = 1,
  status,
  b1 = 0,
  b2 = 0
)

Arguments

group	a character string. Two options: sudo or docker, depending to which group the user belongs
scratch.folder	a character string indicating the path of the scratch folder
file	a character string indicating the path of the file, with file name and extension included
nCluster	nCluster interested for the analysis
separator	separator used in count file, e.g. '\t', ','
lfn	name of the list of genes
geneNameControl	0 if the matrix has gene name without ENSEMBL geneID. 1 if the gene names is formatted as: ENSMUSG00000000001:Gnai3. If the gene names is made only by ensamble name, scannoByGtf has to be run first.
status	0 if is raw count, 1 otherwise
b1	the lower range of signal in the heatmap,for negative value write "/-5". To ask the function to do automatic value assignment set 0
b2	the upper range of signal in the heatmap,for negative value write "/-2". To ask the function to do automatic value assignment set 0

Value

stability plot for each nCluster,two files with score information for each cell for each permutation.

Author(s)

Luca Alessandri , alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino

Examples

## Not run: 
hfc("docker","/home/lucastormreig/scratch/","/home/lucastormreig/CASC7.2/6_1hfc/Data/random_10000_filtered_annotated_lorenz_naive_penta2_0",6,",","naive")#

## End(Not run)

kendomaniac/rCASC documentation built on July 3, 2024, 6:05 a.m.