SquareView: Scatter plot of 9-Square

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

Description

Plot a scatter plot with Control beta score as x-axis and Treatment beta score as y-axis, and colored treatment related genes.

Usage

SquareView(
  beta,
  ctrlname = "Control",
  treatname = "Treatment",
  label = 0,
  label.top = TRUE,
  top = 5,
  genelist = c(),
  x_cutoff = NULL,
  y_cutoff = NULL,
  intercept = NULL,
  groups = c("midleft", "topcenter", "midright", "bottomcenter"),
  groupnames = paste0("Group", 1:length(groups)),
  main = NULL,
  filename = NULL,
  width = 6,
  height = 4,
  ...
)

Arguments

beta	Data frame, including columns of ctrlname and treatname, with Gene Symbol as rowname.
ctrlname	A character, specifying the names of control samples.
treatname	A character, specifying the name of treatment samples.
label	An integer or a character specifying the column used as the label, default value is 0 (row names).
label.top	Boolean, whether label the top selected genes, default label the top 10 genes in each group.
top	Integer, specifying the number of top selected genes to be labeled. Default is 5.
genelist	Character vector, specifying labeled genes.
x_cutoff	An one or two-length numeric vector, specifying the cutoff used for x-axis.
y_cutoff	An one or two-length numeric vector, specifying the cutoff used for y-axis.
intercept	An one or two-length numeric vector, specifying the intercept of diagonal.
groups	A character vector, specifying which group to be colored. Optional groups include "topleft", "topcenter", "topright", "midleft", "midright", "bottomleft", "bottomcenter", "bottomright".
groupnames	A character vector, specifying group names.
main	As in 'plot'.
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

See Also

ScatterView

Examples

file3 = file.path(system.file("extdata", package = "MAGeCKFlute"),
"testdata/mle.gene_summary.txt")
dd = ReadBeta(file3)
SquareView(dd, ctrlname = "dmso", treatname = "plx", label = "Gene")

MAGeCKFlute documentation built on Nov. 8, 2020, 5:40 p.m.