PlotProfiles {maSigPro}R Documentation

Function for visualization of gene expression profiles

Description

PlotProfiles displays the expression profiles of a group of genes.

Usage

PlotProfiles(data, cond, main = NULL, cex.xaxis = 0.5, ylim = NULL, 
    repvect, sub = NULL, color.mode = "rainbow") 

Arguments

data a matrix containing the gene expression data
cond vector for x axis labeling, typically array names
main plot main title
cex.xaxis graphical parameter maginfication to be used for x axis in plotting functions
ylim index vector indicating experimental replicates
repvect index vector indicating experimental replicates
sub plot subtitle
color.mode color scale for plotting profiles. Can be either "rainblow" or "gray"

Details

The repvect argument is used to indicate with vertical lines groups of replicated arrays.

Value

Plot of experiment-wide gene expression profiles.

Author(s)

Ana Conesa, aconesa@ivia.es, Maria Jose Nueda, mj.nueda@ua.es

References

Conesa, A., Nueda M.J., Alberto Ferrer, A., Talon, T. 2005. maSigPro: a Method to Identify Significant Differential Expression Profiles in Time-Course Microarray Experiments.

See Also

PlotGroups

Examples

#### GENERATE TIME COURSE DATA
## generate n random gene expression profiles of a data set with 
## one control plus 3 treatments, 3 time points and r replicates per time point.

tc.GENE <- function(n, r,
             var11 = 0.01, var12 = 0.01,var13 = 0.01,
             var21 = 0.01, var22 = 0.01, var23 =0.01,
             var31 = 0.01, var32 = 0.01, var33 = 0.01,
             var41 = 0.01, var42 = 0.01, var43 = 0.01,
             a1 = 0, a2 = 0, a3 = 0, a4 = 0,
             b1 = 0, b2 = 0, b3 = 0, b4 = 0,
             c1 = 0, c2 = 0, c3 = 0, c4 = 0)
{

  tc.dat <- NULL
  for (i in 1:n) {
    Ctl <- c(rnorm(r, a1, var11), rnorm(r, b1, var12), rnorm(r, c1, var13))  # Ctl group
    Tr1 <- c(rnorm(r, a2, var21), rnorm(r, b2, var22), rnorm(r, c2, var23))  # Tr1 group
    Tr2 <- c(rnorm(r, a3, var31), rnorm(r, b3, var32), rnorm(r, c3, var33))  # Tr2 group
    Tr3 <- c(rnorm(r, a4, var41), rnorm(r, b4, var42), rnorm(r, c4, var43))  # Tr3 group
    gene <- c(Ctl, Tr1, Tr2, Tr3)
    tc.dat <- rbind(tc.dat, gene)
  }
  tc.dat
}

## create 10 genes with profile differences between Ctl, Tr2, and Tr3 groups
tc.DATA <- tc.GENE(n = 10,r = 3, b3 = 0.8, c3 = -1, a4 = -0.1, b4 = -0.8, c4 = -1.2)
rownames(tc.DATA) <- paste("gene", c(1:10), sep = "")
colnames(tc.DATA) <- paste("Array", c(1:36), sep = "")

PlotProfiles (tc.DATA, cond = colnames(tc.DATA), main = "Time Course", 
              repvect = rep(c(1:12), each = 3))


[Package maSigPro version 1.14.0 Index]