scEnhancedVolcano: scEnhancedVolcano

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

scEnhancedVolcano

Description

This function creates an enhanced volcano plot.

Usage

scEnhancedVolcano(
  toptable,
  x = "avg_log2FC",
  y = "p_val_adj",
  lab = rownames(toptable),
  title = paste("DGEA"),
  selectLab = trail(lab, 10),
  min.p = 1e-50,
  max.l2fc = Inf,
  min.pct.cells = 0.1,
  pCutoffCol = "p_val_adj",
  pCutoff = 0.001,
  FCcutoff = 1,
  suffix = NULL,
  caption = paste("Min. Fold Change in Input:", .estMinimumFC(toptable)),
  caption2 = paste("min p_adj:", min.p, "(Y-axis values clipped at)"),
  count_stats = TRUE,
  drawConnectors = TRUE,
  max.overlaps = Inf,
  h = 9,
  w = h,
  ...
)

Arguments

toptable	A data frame with the results of differential gene expression analysis.
x	The x-axis, which is typically the average log2 fold change.
y	The y-axis, which is typically the adjusted p-value.
lab	A vector of gene symbols to label on the plot.
title	The title of the plot.
selectLab	A vector of gene symbols to select for labeling.
min.p	The minimum p-value, to trim high values on the Y-axis.
max.l2fc	The maximum log2 fold change, to trim high values on the X-axis.
min.pct.cells	The minimum percentage of cells in which a gene must be expressed to be included in the plot.
pCutoffCol	The column in the toptable that contains the p-value cutoff.
pCutoff	The p-value cutoff.
FCcutoff	The fold change cutoff.
suffix	A string to append to the filename/title of the plot.
caption	The first line of caption of the plot.
caption2	The second line of caption of the plot.
count_stats	Logical. Calculates a data frame with the count statistics.
drawConnectors	Whether to draw connectors between the labels and the points.
max.overlaps	The maximum number of labels that can overlap.
h	The height of the plot.
w	The width of the plot.
...	Pass any other parameter to EnhancedVolcano::EnhancedVolcano().

Value

A ggplot object.

vertesy/Seurat.utils documentation built on Dec. 4, 2024, 5:20 p.m.