VolcanoPlot: VolcanoPlot

In zh542370159/SCP: Single Cell Pipeline

VolcanoPlot

Description

Generate a volcano plot based on differential expression analysis results.

Usage

VolcanoPlot(
  srt,
  group_by = NULL,
  test.use = "wilcox",
  DE_threshold = "avg_log2FC > 0 & p_val_adj < 0.05",
  x_metric = "diff_pct",
  palette = "RdBu",
  palcolor = NULL,
  pt.size = 1,
  pt.alpha = 1,
  cols.highlight = "black",
  sizes.highlight = 1,
  alpha.highlight = 1,
  stroke.highlight = 0.5,
  nlabel = 5,
  features_label = NULL,
  label.fg = "black",
  label.bg = "white",
  label.bg.r = 0.1,
  label.size = 4,
  aspect.ratio = NULL,
  xlab = x_metric,
  ylab = "-log10(p-adjust)",
  theme_use = "theme_scp",
  theme_args = list(),
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE
)

Arguments

srt	An object of class 'SummarizedExperiment' containing the results of differential expression analysis.
group_by	A character vector specifying the column in 'srt' to group the samples by. Default is 'NULL'.
test.use	A character string specifying the type of statistical test to use. Default is "wilcox".
DE_threshold	A character string specifying the threshold for differential expression. Default is "avg_log2FC > 0 & p_val_adj < 0.05".
x_metric	A character string specifying the metric to use for the x-axis. Default is "diff_pct".
palette	A character string specifying the color palette to use for the plot. Default is "RdBu".
palcolor	A character string specifying the color for the palette. Default is 'NULL'.
pt.size	A numeric value specifying the size of the points. Default is 1.
pt.alpha	A numeric value specifying the transparency of the points. Default is 1.
cols.highlight	A character string specifying the color for highlighted points. Default is "black".
sizes.highlight	A numeric value specifying the size of the highlighted points. Default is 1.
alpha.highlight	A numeric value specifying the transparency of the highlighted points. Default is 1.
stroke.highlight	A numeric value specifying the stroke width for the highlighted points. Default is 0.5.
nlabel	An integer value specifying the number of labeled points per group. Default is 5.
features_label	A character vector specifying the feature labels to plot. Default is 'NULL'.
label.fg	A character string specifying the color for the labels' foreground. Default is "black".
label.bg	A character string specifying the color for the labels' background. Default is "white".
label.bg.r	A numeric value specifying the radius of the rounding of the labels' background. Default is 0.1.
label.size	A numeric value specifying the size of the labels. Default is 4.
aspect.ratio	A numeric value specifying the aspect ratio of the plot. Default is 'NULL'.
xlab	A character string specifying the x-axis label. Default is the value of 'x_metric'.
ylab	A character string specifying the y-axis label. Default is "-log10(p-adjust)".
theme_use	A character string specifying the theme to use for the plot. Default is "theme_scp".
theme_args	A list of theme arguments to pass to the 'theme_use' function. Default is an empty list.
combine	A logical value indicating whether to combine the plots for each group into a single plot. Default is 'TRUE'.
nrow	An integer value specifying the number of rows in the combined plot. Default is 'NULL'.
ncol	An integer value specifying the number of columns in the combined plot. Default is 'NULL'.
byrow	A logical value indicating whether to arrange the plots by row in the combined plot. Default is 'TRUE'.

See Also

RunDEtest

Examples

data("pancreas_sub")
pancreas_sub <- RunDEtest(pancreas_sub, group_by = "CellType", only.pos = FALSE)
VolcanoPlot(pancreas_sub, group_by = "CellType")
VolcanoPlot(pancreas_sub, group_by = "CellType", DE_threshold = "abs(diff_pct) > 0.3 & p_val_adj < 0.05")
VolcanoPlot(pancreas_sub, group_by = "CellType", x_metric = "avg_log2FC")

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.