RankView: View the rank of gene points

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

Description

Rank all genes according to beta score deviation, and label top and bottom meaningful genes. Some other interested genes can be labeled too.

Usage

RankView(
  rankdata,
  genelist = NULL,
  top = 10,
  bottom = 10,
  cutoff = NULL,
  main = NULL,
  filename = NULL,
  width = 5,
  height = 4,
  ...
)

Arguments

rankdata	Numeric vector, with gene as names.
genelist	Character vector, specifying genes to be labeled in figure.
top	Integer, specifying number of top genes to be labeled.
bottom	Integer, specifying number of bottom genes to be labeled.
cutoff	Numeric.
main	As in 'plot'.
filename	Figure file name to create on disk. Default filename="NULL", which means no output.
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

file1 = file.path(system.file("extdata", package = "MAGeCKFlute"),
"testdata/rra.gene_summary.txt")
gdata = ReadRRA(file1)
rankdata = gdata$Score
names(rankdata) = gdata$id
RankView(rankdata)

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