plotVar.mcia {omicade4} | R Documentation |
mcia
Plot variable space of mcia
and visualize selected
variables across datasets, the function is called by plotVar
.
## S3 method for class 'mcia' plotVar(x, var = NA, axes = 1:2, var.col = "red", var.lab = FALSE, bg.var.col = "gray", nlab = 0, sepID.data=NULL, sepID.sep= "\\.", df = NA, layout = NA, ...)
x |
An object of class |
var |
see |
axes |
see |
var.col |
see |
var.lab |
see |
bg.var.col |
see |
nlab |
see |
sepID.data |
see |
sepID.sep |
see |
df |
Integers indicating which dataset should be plotted, the default NA means all datasets are plotted. |
layout |
The layout of multiple plots. |
... |
Other arguments |
If var
is not NA, a data frame is return, with rows for variables of
interest and columns of logical values indicating which data.frames contains which
variables.
Chen Meng
See Also as plotVar.cia
, plotVar
data(NCI60_4arrays) mcoin <- mcia(NCI60_4arrays) plot.mcia(mcoin, sample.lab=FALSE, df.col=4:7) plotVar(mcoin, var=NA, bg.var.col=1:4, var.lab=TRUE) plotVar(mcoin, var=c("SPOPL", "CAPN2", "SNX8"), df=1:4, var.lab=TRUE, var.col=c("red", "green", "blue")) data(NCI60_4arrays) mcoin <- mcia(NCI60_4arrays) plotVar(mcoin, var=c("S100B", "S100A1"), var.lab=TRUE) # an example for the usage of sepID.data and sepID.sep nci60_mod <- NCI60_4arrays rownames(nci60_mod$hgu95) <- paste(rownames(nci60_mod$hgu95), "s1", sep="_") mcoin_mod <- mcia(nci60_mod) id <- split(rownames(mcoin_mod$mcoa$Tco), mcoin_mod$mcoa$TC$T) sapply(id, function(x) head(x)) plotVar(mcoin_mod, var=c("S100B", "S100A1"), var.lab=TRUE, sepID.data=1:4, sepID.sep = c("\\.", "\\.", "\\.", "_")) plotVar(mcoin_mod, var=c("S100B", "S100A1"), var.lab=TRUE, sepID.data=4, sepID.sep="_") plotVar(mcoin_mod, var=c("S100B", "S100A1"), var.lab=TRUE, sepID.data=1:3, sepID.sep="\\.")