enhance_table {GeneTonic} | R Documentation |
Creates a visual summary for the results of a functional enrichment analysis, by displaying also the components of each gene set and their expression change in the contrast of interest
enhance_table( res_enrich, res_de, annotation_obj, n_gs = 50, gs_ids = NULL, chars_limit = 70, plot_title = NULL )
res_enrich |
A |
res_de |
A |
annotation_obj |
A |
n_gs |
Integer value, corresponding to the maximal number of gene sets to be displayed. |
gs_ids |
Character vector, containing a subset of |
chars_limit |
Integer, number of characters to be displayed for each geneset name. |
plot_title |
Character string, used as title for the plot. If left |
A ggplot
object
library("macrophage") library("DESeq2") library("org.Hs.eg.db") library("AnnotationDbi") # dds object data("gse", package = "macrophage") dds_macrophage <- DESeqDataSet(gse, design = ~line + condition) rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15) dds_macrophage <- estimateSizeFactors(dds_macrophage) # annotation object anno_df <- data.frame( gene_id = rownames(dds_macrophage), gene_name = mapIds(org.Hs.eg.db, keys = rownames(dds_macrophage), column = "SYMBOL", keytype = "ENSEMBL"), stringsAsFactors = FALSE, row.names = rownames(dds_macrophage) ) # res object data(res_de_macrophage, package = "GeneTonic") res_de <- res_macrophage_IFNg_vs_naive # res_enrich object data(res_enrich_macrophage, package = "GeneTonic") res_enrich <- shake_topGOtableResult(topgoDE_macrophage_IFNg_vs_naive) res_enrich <- get_aggrscores(res_enrich, res_de, anno_df) enhance_table(res_enrich, res_de, anno_df, n_gs = 10)