hfc.Rd
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 )
group, | a character string. Two options: sudo or docker, depending to which group the user belongs |
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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 |
stability plot for each nCluster,two files with score information for each cell for each permutation.
Luca Alessandri , alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino
if (FALSE) { hfc("docker","/home/lucastormreig/scratch/","/home/lucastormreig/CASC7.2/6_1hfc/Data/random_10000_filtered_annotated_lorenz_naive_penta2_0",6,",","naive")# }