heatmapGO {autoGO} | R Documentation |
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)