plot_general.heatmap: plot_general.heatmap

In seriph78/COTAN_stable: COexpression Tables ANalysis

Description

This function is used to plot an heatmap made using only some genes, as markers, and collecting all other genes correlated with these markers with a p-value smaller than the set threshold. Than all relations are plotted. Primary markers will be plotted as groups of rows. Markers list will be plotted as columns.

Usage

plot_general.heatmap(
  prim.markers = c("Satb2", "Bcl11b", "Cux1", "Fezf2", "Tbr1"),
  markers.list = c(),
  dir,
  condition,
  p_value = 0.001,
  symmetric = TRUE
)

## S4 method for signature 'ANY'
plot_general.heatmap(
  prim.markers = c("Satb2", "Bcl11b", "Cux1", "Fezf2", "Tbr1"),
  markers.list = c(),
  dir,
  condition,
  p_value = 0.001,
  symmetric = TRUE
)

Arguments

prim.markers	A set of genes plotted as rows.
markers.list	A set of genes plotted as columns.
dir	The directory where the COTAN object is stored.
condition	The prefix for the COTAN object file.
p_value	The p-value threshold
symmetric	A boolean: default F. If T the union of prim.markers and marker.list is sets as both rows and column genes

Value

A ggplot2 object

Examples

## Not run: 
plot_general.heatmap(dir=input_dir,
condition = "E17.5",
prim.markers  = c("Mef2c","Mef2a","Mef2d"),
symmetric = FALSE,
markers.list = c("Reln","Satb2","Cux1","Bcl11b","Tbr1","Sox5","Foxp2","Slc17a6","Slc17a7"),
p_value = 0.05)

## End(Not run)

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