MAView: MAplot of gene beta scores

In WubingZhang/MAGeCKFlute: Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

MAplot of gene beta scores

Description

MAplot of gene beta scores in Control vs Treatment

Usage

MAView(
  beta,
  ctrlname = "Control",
  treatname = "Treatment",
  main = NULL,
  show.statistics = TRUE,
  add.smooth = TRUE,
  lty = 1,
  smooth.col = "red",
  plot.method = c("loess", "lm", "glm", "gam"),
  filename = NULL,
  width = 5,
  height = 4,
  ...
)

Arguments

beta	Data frame, including ctrlname and treatname as columns.
ctrlname	Character vector, specifying the name of control sample.
treatname	Character vector, specifying the name of treatment sample.
main	As in plot.
show.statistics	Show statistics .
add.smooth	Whether add a smooth line to the plot.
lty	Line type for smooth line.
smooth.col	Color of smooth line.
plot.method	A string specifying the method to fit smooth line, which should be one of "loess" (default), "lm", "glm" and "gam".
filename	Figure file name to create on disk. Default filename="NULL", which means don't save the figure on disk.
width	As in ggsave.
height	As in ggsave.
...	Other available parameters in function 'ggsave'.

Value

An object created by ggplot, which can be assigned and further customized.

Author(s)

Wubing Zhang

Examples

file3 = file.path(system.file("extdata", package = "MAGeCKFlute"),
"testdata/mle.gene_summary.txt")
dd = ReadBeta(file3)
MAView(dd, ctrlname = "Pmel1_Ctrl", treatname = "Pmel1")
dd2 = NormalizeBeta(dd, method="loess", org = "mmu")
MAView(dd2, ctrlname = "Pmel1_Ctrl", treatname = "Pmel1")

WubingZhang/MAGeCKFlute documentation built on Jan. 27, 2024, 2:43 p.m.