EnrichedGeneView {MAGeCKFlute} | R Documentation |
Visualize enriched pathways and genes in those pathways
EnrichedGeneView( enrichment, geneList, rank_by = "p.adjust", top = 5, bottom = 0, keytype = "Symbol", gene_cutoff = c(-log2(1.5), log2(1.5)), custom_gene = NULL, charLength = 40, filename = NULL, width = 7, height = 5, ... )
enrichment |
A data frame of enrichment result or an |
geneList |
A numeric geneList used in enrichment anlaysis. |
rank_by |
"p.adjust" or "NES", specifying the indices for ranking pathways. |
top |
An integer, specifying the number of positively enriched terms to show. |
bottom |
An integer, specifying the number of negatively enriched terms to show. |
keytype |
"Entrez" or "Symbol". |
gene_cutoff |
A two-length numeric vector, specifying cutoff for genes to show. |
custom_gene |
A character vector (gene names), customizing genes to show. |
charLength |
Integer, specifying max length of enriched term name to show as coordinate lab. |
filename |
Figure file name to create on disk. Default filename="NULL", which means no output. |
width |
As in ggsave. |
height |
As in ggsave. |
... |
Other available parameters in ggsave. |
An object created by ggplot
, which can be assigned and further customized.
Wubing Zhang
data(geneList, package = "DOSE") ## Not run: enrichRes <- enrich.GSE(geneList, keytype = "Entrez") EnrichedGeneView(enrichment=slot(enrichRes, "result"), geneList, keytype = "Entrez") ## End(Not run)