From this helpful thread in the bioconductor mailing list.
x <- 1:50 ## these would be your genes set.seed(1) y <- matrix(rnorm(1e4), nc=200) ## this would be your gene expr matrix col <- rgb(190, 190, 190, alpha=60, maxColorValue=255) matplot(x, y, type='l', col=col)
Just to see what it is doing, I made a simpler example
#variable with 2 rows one <- 1:2 #matrix with 2 rows and 10 columns two <- matrix(rnorm(20), nc=10) two # [,1] [,2] [,3] [,4] [,5] [,6] [,7] #[1,] -0.6822078 -0.25108283 2.425193 -0.05766436 -2.6879801 0.3658529 -1.987125 #[2,] -1.0733665 -0.01278288 -1.403296 -0.13803471 -0.5859938 0.4553595 -1.395202 # [,8] [,9] [,10] #[1,] -0.281798 1.8890190 1.0734526 #[2,] -1.498866 0.1831983 -0.4870297 #plots each column in the matrix two, along x matplot(one,two,type='l')
Column 5 of the matrix "two" can most easily be seen as the dotted aqua line (from -2.6879801 to -0.5859938).
This plot could be useful if you wanted to depict the gene expression of 50 genes at 10 timepoints in a timecourse experiment (make a matrix of 10 rows by 50 columns).
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