SquareView: Scatter plot showing dots in 9 quadrants

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

Scatter plot showing dots in 9 quadrants

Description

Scatter plot showing dots in 9 quadrants

Usage

SquareView(
  df,
  ctrlname = "Control",
  treatname = "Treatment",
  label = 0,
  label.top = TRUE,
  top = 5,
  genelist = c(),
  x_cut = NULL,
  y_cut = NULL,
  slope = 1,
  intercept = NULL,
  auto_cut = FALSE,
  auto_cut_x = auto_cut,
  auto_cut_y = auto_cut,
  auto_cut_diag = auto_cut,
  groups = c("midleft", "topcenter", "midright", "bottomcenter"),
  groupnames = paste0("Group", 1:length(groups)),
  legend.position = "none",
  main = NULL,
  filename = NULL,
  width = 6,
  height = 4,
  ...
)

Arguments

df	A data frame.
ctrlname	A character, specifying the names of control samples, of which the average scores will show as the x-axis.
treatname	A character, specifying the name of treatment samples, of which the average scores will show as the y-axis.
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 genes to be labeled.
x_cut	An one or two-length numeric vector, specifying the cutoff used for x-axis.
y_cut	An one or two-length numeric vector, specifying the cutoff used for y-axis.
slope	A numberic value indicating slope of the diagonal cutoff.
intercept	A numberic value indicating intercept of the diagonal cutoff.
auto_cut	Boolean (2-fold SD by default) or numeric, specifying how many standard deviation will be used as cutoff.
auto_cut_x	Boolean (2-fold SD by default) or numeric, specifying how many standard deviation will be used as cutoff on x-axis.
auto_cut_y	Boolean (2-fold SD by default) or numeric, specifying how many standard deviation will be used as cutoff on y-axis
auto_cut_diag	Boolean (2-fold SD by default) or numeric, specifying how many standard deviation will be used as cutoff on 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.
legend.position	Position of the legend.
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 = "Pmel1_Ctrl", treatname = "Pmel1", label = "Gene")

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