miko_volcano: Draw volcano plot to visualize differential expression.

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Draw volcano plot to visualize differential expression.

Description

Draw volcano plot to visualize differential expression. Uses data.frame output from getDEG(..., return.list = F).

Usage

miko_volcano(
  df.deg,
  group = NULL,
  show.n = 10,
  show.sig.only = T,
  rank.by = c("auc", "logFC", "pval"),
  features = NULL,
  sig.threshold = 0.05,
  lfc.threshold = 0,
  label.size = NA,
  pt.size.range = c(1, 4),
  correct.p.value = T,
  plot.title = "Volcano Plot",
  cols = list(low = scales::muted("blue"), mid = "white", high = scales::muted("red"))
)

Arguments

df.deg	Differential expression data. Dataframe output from presto::wilcoxauc() or scMiko::getDEG(..., return.list = F).
group	group to visaulize data for. Must be entry in 'group' column of df.deg.
show.n	Top n features to label. Default is 10.
show.sig.only	Show significant genes only. Default is T.
rank.by	statistic to rank features by when selecting top feature to label. Default is "auc" (options include "auc", "logFC", "pval").
features	Specific features to label. If specified, show.n is ignored.
sig.threshold	significance (p-value) threshold. Default is 0.05.
lfc.threshold	log fold change (lfc) threhsold. Default is 0.
label.size	Label size.
pt.size.range	vector with two values, the first representing the smallest point size, and the second representing the largest point size. Default is c(1,4).
correct.p.value	use adjusted p-value (FDR) for thresholding significant hits. Default is T.
plot.title	title of volcano plot. Default is "Volcano Plot".
cols	named listed with 3 entries labeled "low", "mid", "high" specifying colors to create a color gradient. Default is list(low = scales::muted("blue"), mid = "white", high = scales::muted("red")).

Value

ggplot handle

See Also

getDEG

Examples

 df.dat <- getDEG(so.query, return.list = F)
 plt.volcano <-  miko_volcano(df.deg = df.dat)

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.