SquareView {MAGeCKFlute} | R Documentation |
Plot a scatter plot with Control beta score as x-axis and Treatment beta score as y-axis, and colored treatment related genes.
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, ... )
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'. |
An object created by ggplot
, which can be assigned and further customized.
Wubing Zhang
file3 = file.path(system.file("extdata", package = "MAGeCKFlute"), "testdata/mle.gene_summary.txt") dd = ReadBeta(file3) SquareView(dd, ctrlname = "dmso", treatname = "plx", label = "Gene")