RNAseq_GSEAheatmaps: Make heatmaps from combined GSEA reports after EdgeR

In CoarfaBCM/derecksLabTools: A tool belt for my work at Coarfa lab Baylor College of Medicine

Make heatmaps from combined GSEA reports after EdgeR

Description

Make heatmaps from combined GSEA reports after EdgeR

Usage

RNAseq_GSEAheatmaps(
  gsea_combined_profiles,
 
    clean_names_regex = "EdgeR\\.TMM_Exact_|EdgeR\\.upperquartile_LRT_RUVr_|\\.rnk\\.NES",
  scale_bounds = NULL,
  reo_order_cols = NULL,
  clust_row = TRUE,
  clust_col = FALSE,
  show_rownames = FALSE,
  show_colnames = FALSE
)

Arguments

gsea_combined_profiles	[type: character, default: NULL] this is a path to a prepared excel file. This file should contian your combined reports (all comparisons from GSEA bound together; use Cristian's tool to combine reports. Then combine these reports into a single excel, each tab represents comparisons per pathway collection.
clean_names_regex	[type: character, default: "EdgeR\.TMM_Exact_|EdgeR\.upperquartile_LRT_RUVr_|\.rnk\.NES"] a regex expression to remove strings from the comparison names. Often comparisons are preceeeded by some prefix of the parameters of which the rank files were created, normalisation etc.
scale_bounds	[type: vector<numeric>, default: NULL] if provided will set the max and min of the scale for heatmaps; affects colour intensity.
reo_order_cols	[type: vector<numeric>, default: NULL] if provided will re-order the columns for every heatmap. You must know the order and number of columns you wish before supplying.
clust_row	[type: logical, default: FALSE] true uses pheatmap's clustering on rows; pathways.
clust_col	[type: logical, default: FALSE] true uses pheatmap's clustering on columns; comparisons.
show_rownames	[type: logical, default: FALSE] true shows the rownames; pathways.
show_colnames	[type: logical, default: FALSE] true shows the column names; comparisons.

Details

Your combined GSEA reports should look something like this:

Examples

path <- system.file(
    "extdata",
    "GSEA-combined-enrichment-profiles.xlsx",
    package = "derecksLabTools"
)

heatmaps <- RNAseq_GSEAheatmaps(
    path,
    scale_bounds = NULL,
    reo_order_cols = NULL,
    clust_row = TRUE,
    clust_col = FALSE,
    show_rownames = TRUE,
    show_colnames = TRUE
)
pdf("./hallmark-enrichment-heatmap.pdf", width = 7, height = 10)
print(heatmaps$hallmark)
dev.off()

CoarfaBCM/derecksLabTools documentation built on April 3, 2022, 10:29 p.m.