Create gene plot — getcountplot • carnation

This function creates the gene plot.

Usage

getcountplot(
  df,
  intgroup = "group",
  factor.levels,
  title = NULL,
  ylab = "Normalized counts",
  color = "gene",
  nrow = 2,
  ymin = NULL,
  ymax = NULL,
  log = TRUE,
  freey = FALSE,
  trendline = "smooth",
  facet = NULL,
  legend = TRUE,
  boxes = TRUE,
  rotate_x_labels = 30
)

Arguments

df: data.frame with gene counts
intgroup: metadata variable to plot on x-axis
factor.levels: levels of intgroup to show on x-axis
title: title of plot
ylab: y-axis label
color: metadata variable to color by
nrow: number of rows to plot if faceting
ymin: y-axis lower limit
ymax: y-axis upper limit
log: should y-axis be log10-transformed?
freey: should y-axes of faceted plots have independent scales?
trendline: type of trendline to draw
facet: metadata variable to facet by
legend: show legend?
boxes: show boxes?
rotate_x_labels: angle to rotate x-axis labels (default=30)

Value

ggplot handle