results_barplot: Plot barplot of enrichment results - plotting -log10...

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

Plot barplot of enrichment results - plotting -log10 (p-value) but cut-off significance is based on FDR where if either linear or top10 FDR threshold the result will be plotted

Description

Plot of cell-type enrichment results from celltype_associations_pipeline.

Usage

results_barplot(
  merged_results,
  title = NULL,
  y_lab = NULL,
  x_lab = "-log10(p-value)",
  fdr_thresh = 0.05,
  y_var = "Celltype",
  x_var = "-log10p",
  fill_var = "EnrichmentMode",
  fill_cols = c("#60A9BD", "#3A62A0"),
  horz_line_p = 0.01,
  sort_celltypes_by = "Top 10%",
  show_plot = TRUE,
  height = 5,
  width = 7,
  dpi = 300,
  save_path = file.path(tempdir(), "MAGMA_Celltyping.barplot.jpg")
)

Arguments

merged_results	Enrichment results generated by celltype_associations_pipeline and merged by merge_results.
title	Plot title.
y_lab	Plot y-axis label.
x_lab	Plot x-axis label.
fdr_thresh	FDR filtering threshold.
y_var	y-axis variable.
x_var	x-axis variable.
fill_var	Fill variable.
fill_cols	The two colours to use for the fill param (Vector).
horz_line_p	add dashed line for a p-value cut-off - default of 0.01
sort_celltypes_by	Sort the order of the cell types in the plot by the enrichment results. Choose to sort by Top 10% or Linear results or set to NULL to avoid sorting. Default is Top 10%.
show_plot	Whether to print the plot.
height	Plot height.
width	Plot width.
dpi	Plot resolution. Also accepts a string input: "retina" (320), "print" (300), or "screen" (72). Applies only to raster output types.
save_path	Path to save plot to.

Value

ggplot object.

Examples

MAGMA_results <- MAGMA.Celltyping::enrichment_results
merged_results <- MAGMA.Celltyping::merge_results(MAGMA_results)
bar <- MAGMA.Celltyping::results_barplot(
    merged_results = merged_results,
    fdr_thresh = 1)  

NathanSkene/MAGMA_Celltyping documentation built on March 5, 2025, 5:44 a.m.