heatmapGO {autoGO}

HeatmapGO

Description

If the analysis has been performed on more conditions it is interest to have a look at the difference in the enrichment results between the groups. This can be performed by heatmapGO().

The function automatically reads all the enrichment results of the chosen database. A heatmap is produced for each database, all the terms are merged together and a filter is applied as follows: only terms with a significant pvalue (i.e. less than padj_threshold) in at least one comparison will be retained and plotted. These plots will be saved in the "Comparison_Heatmap" folder. In order to have readable plots, if many terms are enriched for a database several images will be created (indexed _1, _2, ...).

Usage

heatmapGO(
  db,
  outfolder = "./results",
  log2FC_threshold = 0,
  padj_threshold = 0.05,
  min_term_per_row = 2,
  which_list = c("up_genes", "down_genes", "up_down_genes", "not_from_DE")
)

Arguments

db

Database of choice to plot the heatmap. It has to be one for which the enrichment analysis has been performed.

outfolder

The name to assign to the folder for output saving. (Default = "./results"). NOTE: please add "/" at the end.

log2FC_threshold

Threshold value for log2(Fold Change) for considering genes as differentially expressed (Default = 0).

padj_threshold

Threshold value for adjusted p-value significance (Defaults to 0.05).

min_term_per_row

Minimum of comparisons or enriched lists on which a certain term must be significant (Defaults to 2).

which_list

One of c("up_genes", "down_genes","up_down_genes", "not_from_DE"): select data to plot. Respectively, only up regulated genes (up_genes), only down regulated genes ("down_genes"), enrichment on both up and down regulated genes (up_down_genes) or select "not_from_DE" if the enrichment will be made on a list of genes that does not come from a differential expression analysis.

Value

No return value. Files will be produced as part of normal execution.

Examples

## Not run: 
heatmapGO(
  db = "GO_Biological_Process_2021",
  outfolder = "./results",
  log2FC_threshold = 0,
  padj_threshold = 0.05,
  min_term_per_row = 3,
  which_list = "down_genes"
)

## End(Not run)