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05c   act1   although   at   attachment   axes   axis   bring   C1039   C186   can   certain   character   col   colnames   Color   colored   decreasing   easily   elp3   emphasize   for   from   function   gcn5   ge   gm   gme   goi   grid   image   in   labels   las   length   life   little   mar   me   mei2   mst1   mst2   ncol   nrow   nuance   numbers   Numbers   of   or   par   pgk1   png   pretty   Ramp   rep   representing   rgb   rownames   seq   series   Sometimes   sort   Starting   straightforward   table   Table   text   the   this   tick   times   to   Use   values   very   want   with   You   you   zym1  

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Table of Numbers to Image

Sometimes you want to bring a little life or nuance to a table of numbers to emphasize certain values. You can do this pretty easily with R, although it's not very straightforward.

Starting with a table of numbers:

               mst1   gcn5  mst2 elp3    gm    ge    me   gme
  mei2         3.00  3.000  1.00 -2.0  4.00  0.20 -1.00  3.00
  SPAC1039.02 -3.00 -2.000 -2.00  1.0 -5.00  0.70  0.90 -3.00
  zym1         5.00 -0.800  0.50 -1.0  0.80 -2.00 -1.00  3.00
  SPAC186.05c  0.40 -4.000 -4.00 -4.0 -5.00 -0.90  0.80 -3.00
  SPAC186.06  -0.50 -3.000 -4.00 -3.0 -3.00 -0.20  2.00 -3.00
  act1         0.10  0.050  0.04 -0.1  0.09 -0.10 -0.07 -0.03
  pgk1        -0.05 -0.002 -0.05 -0.2  0.02 -0.05 -0.20  0.06

Use the R image() function to create a colored grid representing the values:

# reverse table so that it displays properly in image
goi.d <- goi.d[sort(1:nrow(goi.d), decreasing=T),]

#------------------------------------------#
#----        Draw the image map        ----#
#------------------------------------------#
# yellow->white->blue   faded
R <- c(rep(1, times=128), seq(1,0.5,length=128))
G <- c(rep(1, times=128), seq(1,0.5,length=128))
B <- c(seq(0.5,1,length=128), rep(1, times=128))

# create a color ramp
ColorRamp <- rgb(R, G, B)

# c(bottom, left, top, right)
# The default is 'c(4, 5, 4, 2) + 0.1'.
par(mar= c(4, 7, 4, 2))

# use image() to draw the color grid
# use t() to transpose the dataframe
# so it display like you see it
image(t(goi.d), col=ColorRamp, axes=F)

# create a set of points to draw labels
# across the image
x <- seq(from=0, to=1, length=ncol(goi.d))
y <- seq(from=0, to=1, length=nrow(goi.d))

# create a vector for placing text values
series <- 1:length(y)

for( i in series ){
   text(x,y[i],labels=as.character(goi.d[i,]))
}

axis(3, labels=colnames(goi.d), at=x, tick=F)
axis(2, at=y, labels=rownames(goi.d), tick=F, las=2)

R Table2Image (last edited 2009-04-01 23:01:04 by ChrisSeidel)