For loop assigns variable while i want to plot something with qplot (R)

Question

So i have the following for loop:

for (Count in 1:19){
  png(paste0(colnames(fdd$rawCounts)[Count], ".pdf"))
  qplot(y = log2(fdd$rawCounts[,Count]), main = colnames(fdd$rawCounts)[Count])
  dev.off()
}

Which should simply plot some count data which i put a head from here:

structure(c(11L, 3L, 12L, 8L, 15L, 2L, 5L, 2L, 8L, 7L, 6L, 10L, 
6L, 1L, 7L, 4L, 2L, 1L, 3L, 0L, 4L, 4L, 2L, 5L, 8L, 0L, 13L, 
4L, 10L, 7L, 2L, 1L, 2L, 4L, 7L, 7L, 14L, 4L, 25L, 17L, 14L, 
16L, 4L, 2L, 5L, 5L, 5L, 2L, 9L, 5L, 11L, 8L, 1L, 4L, 10L, 8L, 
8L, 7L, 9L, 5L, 9L, 15L, 14L, 11L, 16L, 8L, 11L, 4L, 3L, 6L, 
3L, 0L, 6L, 3L, 4L, 6L, 1L, 4L, 11L, 11L, 12L, 6L, 2L, 6L, 7L, 
9L, 22L, 8L, 13L, 7L, 6L, 1L, 4L, 5L, 6L, 2L, 4L, 2L, 6L, 7L, 
3L, 2L, 6L, 3L, 3L, 2L, 5L, 5L, 9L, 2L, 6L, 5L, 4L, 2L), .Dim = c(6L, 
19L), .Dimnames = structure(list(feature = c("chr10:100000001-100000500", 
"chr10:10000001-10000500", "chr10:1000001-1000500", "chr10:100000501-100001000", 
"chr10:100001-100500", "chr10:100001001-100001500"), sample = c("K562_FAIRE_Acla_4hr_1", 
"K562_FAIRE_Acla_4hr_2", "K562_FAIRE_Daun_4hr_1", "K562_FAIRE_Daun_4hr_2", 
"K562_FAIRE_Etop_4hr_1", "K562_FAIRE_Etop_4hr_2", "K562_FAIRE_untreated", 
"FAIRE.seq_K562_2MethylDoxo_A", "FAIRE.seq_K562_2MethylDoxo_B", 
"FAIRE.seq_K562_Ctr_A", "FAIRE.seq_K562_Ctr_B", "FAIRE.seq_K562_Doxo_10uM_4hrs_A", 
"FAIRE.seq_K562_Doxo_10uM_4hrs_B", "FAIRE.seq_K562_Epirubicin_A", 
"FAIRE.seq_K562_Epirubicin_B", "FAIRE.seq_K562_MTX_40uM_4hrs_A", 
"FAIRE.seq_K562_MTX_40uM_4hrs_B", "FAIRE.seq_K562_MTX_5uM_4hrs_A", 
"FAIRE.seq_K562_MTX_5uM_4hrs_B")), .Names = c("feature", "sample"
)))

Now if i try to plot the data it gives me a variable called Count and the value is 19L. While i expect 19 plots to be drawn. Why is this happening?

Thanks!

The variable count was created during the to increment through the for loop. — lmo
– lmo, Commented Jun 28, 2016 at 13:07
You should expect to have a variable Count with value 19L since you loop on a variable called Count (which is incidentally defined in the global env) which takes value 1 to, lastly, 19. 19L is just the integer version of 19 (which is just a numeric). So this is not really related to your issue. It would happen even if the png were created. Are you sure this is not working, did you look into your working directory (see getwd)? — asachet
– asachet, Commented Jun 28, 2016 at 13:08
Your example is not reproducible since the data you share is not the fdd your code refer to. BTW some characters cannot appear in filenames, Windows is especially picky about this, so check that your colnames (which become your filenames) are clean of special characters. — asachet
– asachet, Commented Jun 28, 2016 at 13:10

lmo · Accepted Answer · 2016-06-28 13:01:26Z

3

This works for me:

for (Count in 1:19){
  pdf(paste0(colnames(df)[Count], ".pdf"))
  print(qplot(y = log2(df[, Count]), main = colnames(df)[Count]))
  dev.off()
}

A couple of changes:

I read in your data as df. It turns out to be a matrix, so I adjusted the subsetting accordingly.
I also wrapped the qplot function in a print function which forces the figure to be created.
Finally, I switched the png function to pdf as that seemed like the files you were trying to create based on the paste0 result.

answered Jun 28, 2016 at 13:01

lmo

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1 Comment

Sander Van der Zeeuw Over a year ago

Thanks, for the input. In fact i wanted to make a pdf but the files became to big, since i have more then 10 mil points. So i madeit PNG but i forgot to replace the suffix. But indeed this works now, thanks for the help!

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