heatmapGO: HeatmapGO

In isabellagrassucci/autogo_cp: Auto-GO: Reproducible, Robust and High Quality Ontology Enrichment Visualizations

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(
  lib,
  where_results = "./",
  outfolder = "results/",
  log2FC_threshold = 0,
  padj_threshold = 0.05,
  which_list = c("up_genes", "down_genes", "up_down_genes", "not_from_DE")
)

Arguments

lib	Database of choice to plot the heatmap. It has to be one for which the enrichment analysis has been performed.
where_results	Specify the folder in which you want to save outputs. (Default = "./"). Note: if you are working with R Notebooks the default working directory (if not specified) is the folder in which the .Rmd is saved.
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).
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.

isabellagrassucci/autogo_cp documentation built on April 10, 2022, 12:05 a.m.