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

Description Usage Arguments Value Author(s) See Also Examples

View source: R/plotVar.mcia.R

Description

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

Usage

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## 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

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  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="\\.")

omicade4 documentation built on May 31, 2017, 12:37 p.m.

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