plot_overlap: Plot gene-annotation matches as heatmap

In AhmedMehdiLab/E.PAGE: Environmental Pathways Affecting Gene Expression

Plot gene-annotation matches as heatmap

Description

Heatmap will plot genes on the X-axis against annotations on the Y-axis. Matches will be shown with colored squares, and non-matches will be transparent. If the value is "Gene Value", "Odds Ratio", "Fold Enrichment" or "Adjusted Fold Enrichment", if the value is NaN or an infinity, these will also be transparent.

Usage

plot_overlap(matches, value, input, stats, xpos = "bottom")

Arguments

matches	value from compute
value	"Gene Value" for values from input or one of "#gene sets", "# genes", "# matches", "P-value", "Adjusted P-value", "Odds Ratio", "Fold Enrichment" or "Adjusted Fold Enrichment" for values from stats
input	output of process_input_text or process_input_seurat
stats	value from compute
xpos	x axis position, "top" or "bottom"

Value

ggplot2: heatmap of overlap

Examples

anno <- E.PATH::annotations
data <- E.PATH::database

input <- process_input_text("FCN1 0.1 FTL 0.8 CLU 0.05")
results <- compute(input, anno, data)
over <- plot_overlap(results$matches, "Gene Value", input, results$stats)

AhmedMehdiLab/E.PAGE documentation built on Aug. 21, 2022, 4:37 p.m.