plotVar.mcia: Plot variable space of result from 'mcia'

In mengchen18/omicade4: Multiple co-inertia analysis of omics datasets

Description

Plot variable space of mcia and visualize selected variables across datasets, the function is called by plotVar.

Usage

## 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, ...)

Arguments

x	An object of class mcia, the result returned by mcia.
var	see plotVar
axes	see plotVar
var.col	see plotVar
var.lab	see plotVar
bg.var.col	see plotVar
nlab	see plotVar
sepID.data	see plotVar
sepID.sep	see plotVar
df	Integers indicating which dataset should be plotted, the default NA means all datasets are plotted.
layout	The layout of multiple plots.
...	Other arguments

Value

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.

Author(s)

Chen Meng

See Also

See Also as plotVar.cia, plotVar

Examples

  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="\\.")

mengchen18/omicade4 documentation built on Nov. 2, 2020, 10:30 a.m.