plot_heatmap: plot_heatmap

In seriph78/COTAN_stable: COexpression Tables ANalysis

Description

This is the function that create the heatmap of one or more COTAN object.

Usage

plot_heatmap(p_val.tr = 0.05, df_genes, sets, conditions, dir)

## S4 method for signature 'ANY'
plot_heatmap(p_val.tr = 0.05, df_genes, sets, conditions, dir)

Arguments

p_val.tr	p-value threshold. Default is 0.05
df_genes	this is a list of gene array. The first array will define genes in the columns.
sets	This is a numeric array indicating from which fields of the previous list will be considered
conditions	An array of prefixes indicating the different files.
dir	The directory in which are all COTAN files (corresponding to the previous prefixes)

Value

a ggplot object

Examples

## Not run: 
# some genes
primary.markers = c("Tbr1","Tubb3","Neurod1", "Stmn1","Notch1","Vim","Sox2","Pax6","Hes5")
a example of named list of different gene set
gene.sets.list = list("primary.markers"=primary.markers,
                   "2.Radial Glia" = c("Vim","Sox2","Pax6","Hes5","Hes1","Fabp7"),
                   "PNGs"=c("Map2","Tubb3","Neurod1","Nefm","Nefl","Dcx","Tbr1"),
                   "constitutive" = c("Calm1","Cox6b1","Ppia","Rpl18","Cox7c",
                                      "Erh","H3f3a","Taf1b","Taf2",
                                      "Gapdh","Actb", "Golph3", "Mtmr12",
                                      "Zfr", "Sub1", "Tars", "Amacr"),
                   "4.Mat.neu."= c("Map2","Rbfox3","Nefl","Nefh","Nefm","Mapt"))
plot_heatmap(p_v = 0.05, df_genes =gene.sets.list ,
sets =c(2,3,4,6) ,conditions =c("E11.5","E13.5","E14.5") ,dir = input_dir)

## End(Not run)

seriph78/COTAN_stable documentation built on Dec. 23, 2021, 12:19 a.m.