Using the reshape module on R

reshape.R

library(reshape)

#suppose I read a file with the header lines of sample and 13 target ids
# the values represent median target coverage from an exome capture experiment
median <- read.table("median.txt", header=T)
> median
  sample t1 t2 t3 t4 t5 t6 t7 t8  t9 t10 t11 t12 t13
1     s1 10 34 31 66 34 61 40 46 117  29  55  96  33
2     s2 20 29 25 36 27 53 34 26  89  28  40  70  26
3     s3  8 31 31 66 33 57 31 36  93  36  40  74  27
4     s4 12 35 40 63 32 70 36 42 149  36  50  98  30
5     s5 12 28 23 31 31 36 36 30  66  33  45  60  26
6     s6 17 33 39 66 30 70 39 44 128  32  53  91  32

#I want to plot on the x-axis the target ids and the y axis the median coverage for each of samples

# Now the table I read has 78 elements. I want to melt the table into a data structure
# with sample, target, median. This can be down easily with the melt function

median.reshape = melt(median)

> median.reshape
         sample target median
1  s1    t1     10
2  s2    t1     20
3  s3    t1      8
4  s4    t1     12

(truncated to save space)

#now plot it
xyplot(median~target, groups=sample, data=median.reshape, type="b", xlab="targets", main="my plot")

#here is a nice tutorial http://www.statmethods.net/management/reshape.html