plotGOHeatmap: Create a heatmap from a compareClusterResult...

In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

Create a heatmap from a compareClusterResult (compareCluster) package) showing for each enriched GO term, the overall observed correlation of the associated genes set.

Description

Create a heatmap from a compareClusterResult (compareCluster) package) showing for each enriched GO term, the overall observed correlation of the associated genes set.

Usage

plotGOHeatmap(compareCluster, level = 5, corrValue, corr = TRUE,
  sortDF = TRUE, simpleHeatmap = TRUE,
  corName = "Pearson\nCorrelation", base_family = "Linux Libertine",
  base_size = 16, stripName = FALSE, out = "DF", plot = TRUE)

Arguments

compareCluster	Result object of compareCluster
level	integer; default: 5. How many level of the comparison between cluster should be retrieved
corrValue	numeric vector. The correlation values for the different GO terms associated gene sets.
corr	logical; default: TRUE. Whether the correlation should be plotted.
sortDF	logical; default: TRUE. Whether the results should be sorted by correlation.
simpleHeatmap	logical; default: TRUE. Whether to remove the GO for which the gene set is empty.
corName	string; default: "Pearson Correlation". Allow to personalise the correlation legend
base_family	string; default: "Linux Libertine". Name of the font family to use for the plot
base_size	numeric; size of the main text of the plot; default: 16
stripName	logical; default: FALSE.
out	string; switch that allows to chose the type result object. default: "DF", gives a data.frame (used for the plot), other options: "mat" gives the previous result formatted as a matrix "plot" gives the figure ready to be saved as an object.
plot	logical; default: TRUE. Whether a plot should outputed to the standard output.

Value

depends of the value of "out"

barzine/barzinePhdR documentation built on Nov. 23, 2024, 8:54 p.m.