plot_overlap: Plot gene-annotation matches as heatmap

In lilin-yang/glacier: Gene List Annotation, Calculation and Illustration of Enrichment in R

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, val_trans = "identity")

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
val_trans	optional: value transformation, see trans argument in scale_continuous; default "identity"

Value

ggplot2: heatmap of overlap

Examples

anno_path <- system.file("extdata", "ex_anno.csv", package = "glacier")
data_path <- system.file("extdata", "ex_data.csv", package = "glacier")
anno <- import_annotations(anno_path, ",", TRUE, c(2, 4), 5)
data <- import_database(data_path, ",", FALSE, c(2, 4), 0)

input <- process_input_text('CYP1A1 0.2 CYP1B1 NQO1 0.3 SODD 9.0')
results <- compute(input, anno, data)
over <- plot_overlap(results$matches, "Gene Value", input, results$stats)

lilin-yang/glacier documentation built on Oct. 3, 2020, 8:06 a.m.