ridgeEnrichment {escape} | R Documentation |
This function allows to the user to examine the distribution of enrichment across groups by generating a ridge plot.
ridgeEnrichment( enriched, group = "cluster", gene.set = NULL, scale.bracket = NULL, facet = NULL, add.rug = FALSE, colors = c("#0348A6", "#7AC5FF", "#C6FDEC", "#FFB433", "#FF4B20") )
enriched |
The output of |
group |
The parameter to group, displayed on the y-axis. |
gene.set |
The gene set to graph on the x-axis. |
scale.bracket |
This will filter the enrichment scores to remove extreme outliers. Values entered (1 or 2 numbers) will be the filtering parameter using z-scores of the selected gene.set. If only 1 value is given, a seocndary bracket is autommatically selected as the inverse of the number. |
facet |
A parameter to separate the graph. |
add.rug |
Binary classifier to add a rug plot to the x-axis. |
colors |
The color palette for the ridge plot. |
ggplot2 object with ridge-based distributions of selected gene.set
enrichIt
for generating enrichment scores.
ES2 <- readRDS(url( "https://ncborcherding.github.io/vignettes/escape_enrichment_results.rds")) ridgeEnrichment(ES2, gene.set = "HALLMARK_DNA_REPAIR", group = "cluster", facet = "Type", add.rug = TRUE)