hfc, heatmap for clustering

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

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

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

Examples

if (FALSE) {
hfc("docker","/home/lucastormreig/scratch/","/home/lucastormreig/CASC7.2/6_1hfc/Data/random_10000_filtered_annotated_lorenz_naive_penta2_0",6,",","naive")#
}