ggvolcano: Volcano plot

In jlaffy/scalop: Single Cell Analysis Operations

Volcano plot

Description

Perform differential expression and create a volcano plot.

Usage

ggvolcano(
  m = NULL,
  group = NULL,
  group2 = NULL,
  dea.res = NULL,
  pmethod = "BH",
  alternative = NULL,
  logp = 2,
  lfc = 1,
  n = 10,
  selected = NULL,
  add.to.selected = NULL,
  selected.col = "red",
  xlab = "Log2 Fold Change",
  ylab = "-Log10 P-value (adjusted)",
  symmetric = TRUE,
  xintercept = 0,
  segment.colour = "grey30",
  text.size = 14,
  label.size = 5,
  legend.text.size = 12,
  ymax = NULL,
  xlim = NULL
)

Arguments

m	A matrix of features (e.g. genes) by observations (e.g. cells). Default: NULL
group	The group (of observations) to test. This should be a character vector or a two-level factor in which the first level corresponds to the group. Default: NULL
group2	A second group to test against. This should be a character vector. If 'group2=NULL', defaults to all remaining observations in the matrix 'm'. Default: NULL
dea.res	The output of scalop::dea(..., return.val = 'df'). If provided, the function will not perform DEA and skip straight to plotting. Default: NULL
pmethod	The correction method for multiple testing, or 'none' if no correction is desired. See stats::p.adjust.methods for options. Default: 'BH'
alternative	The alternative hypothesis. If 'alternative=NULL' and 'group2' was provided, defaults to 'two-sided'. Else defaults to 'greater'. Default: NULL
logp	The minimum -log10(P) value at which differential expression is considered significant. Default: 2
lfc	The minimum log2 foldchange value at which differential expression is considered signficant. Default: 1
n	The number of top features to display. Default: 10
selected	Default: NULL
add.to.selected	PARAM_DESCRIPTION, Default: NULL
selected.col	PARAM_DESCRIPTION, Default: 'red'
xlab	X-axis title. Default: 'Log2 Fold Change'
ylab	Y-axis title. Default: '-Log10 P-value (adjusted)'
symmetric	PARAM_DESCRIPTION, Default: TRUE
xintercept	One or more numeric values to be added as vertical delimiters to the plot. Default: 0
text.size	Axes text size. Default: 14
label.size	Feature label text sizes. Default: 5
legend.text.size	Legend text size. Default: 12
ymax	Y-axis upper limit. If 'NULL', defaults to the maximum -log10(P) value. Setting 'ymax' can be useful to 'zoom in' on the y-axis, making feature points/labels below 'ymax' easier to see. Default: NULL
xlim	PARAM_DESCRIPTION, Default: NULL

Details

DETAILS

Value

A list containing:

• data: A data frame; the differential expression results used in the plotting.

• G: A ggplot2 object; the volcano plot.

See Also

mutate,filter,arrange,pull ggplot,geom_point,scale_continuous,ggtheme,theme,labs,scale_manual,geom_abline geom_text_repel

Examples

## Not run: 
if(interactive()){
 #EXAMPLE1
 }

## End(Not run)

jlaffy/scalop documentation built on March 24, 2024, 9 a.m.