plot_volcano: Plot volcano plot with annotations

In keshav-motwani/scanalysis: Multi-Sample Visualization and Immune Repertoire Analysis Utilities for Single-Cell Data

Description

Plot volcano plot with annotations

Usage

plot_volcano(
  data,
  fold_change,
  p_value,
  color = NULL,
  label = "gene",
  annotations = c(),
  annotations_if_threshold = c(),
  annotations_if_column = NULL,
  n_annotate_top = 10,
  p_value_threshold = 0.05,
  fold_change_threshold = 1.5,
  p_value_rank_threshold = 100,
  rank_by = "p_value",
  alpha = 0.5,
  facet_rows = c(),
  facet_columns = c(),
  facet_type = "grid",
  ...
)

Arguments

data	differential expression results
fold_change	column containing fold change data (x-axis)
p_value	column containing p-value data (y-axis is -log10(p_value))
color	column for color
label	column for text annotation
annotations	features to be annotated
annotations_if_threshold	features to be annotated iff they meet the thresholds
n_annotate_top	number of top DE genes to annotate
p_value_threshold	maximum p-value
fold_change_threshold	minimum absolute fold change threshold
p_value_rank_threshold	maximum p-value rank threshold
alpha	alpha of points
facet_rows	columns for faceting by row
facet_columns	columns for faceting by column
facet_type	either "wrap" or "grid", corresponding to facet_wrap and facet_grid respectively
...	other params passed into either facet_wrap or facet_grid, depending on facet_type parameter

Value

ggplot2 object

Examples

NULL

keshav-motwani/scanalysis documentation built on Feb. 4, 2021, 2:21 a.m.