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(), scale_cutoff = 1.96, main = NULL, filename = NULL, width = 5, height = 4, ...)
beta |
Data frame, including columns of |
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. |
scale_cutoff |
Numeric, specifying the number of standard deviation to be used as cutoff. |
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
data(mle.gene_summary) # Read beta score from gene summary table in MAGeCK MLE results dd = ReadBeta(mle.gene_summary, organism="hsa") SquareView(dd, ctrlname = "dmso", treatname = "plx", label = "Gene")