gs_summary_overview {GeneTonic} | R Documentation |
Plots a summary of enrichment results for one set
gs_summary_overview( res_enrich, n_gs = 20, p_value_column = "gs_pvalue", color_by = "z_score", return_barchart = FALSE )
res_enrich |
A |
n_gs |
Integer value, corresponding to the maximal number of gene sets to be displayed |
p_value_column |
Character string, specifying the column of |
color_by |
Character, specifying the column of |
return_barchart |
Logical, whether to return a barchart (instead of the default dot-segment plot); defaults to FALSE. |
A ggplot
object
gs_summary_overview_pair()
, gs_horizon()
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) gs_summary_overview(res_enrich) # if desired, it can also be shown as a barplot gs_summary_overview(res_enrich, 30, return_barchart = TRUE)