Hello,
I'm trying to figure out how to draw combined average profile graphs in R. I have 4 files, each with 2 columns of values. Any help given would be useful. Thank you.
The most convenient method is to just use ggplot2. If you make a single data.frame from your 4 files and add a column that designates what column things came from then just:
g <- ggplot(some_data_frame, aes(x=position, y=average_value, colour=some_file_designator))
g <- g + geom_line()
g
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version 2.3.6
Hello anjanaram1!
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This belongs better on stackoverflow (or its statistics division).
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the two values are "TSS binding site affinities" vs. log likelihood ratios.
Even so, this is more of a graphing question than bioinformatics. Have you tried searching on stack overflow?
Yes I have. I'm trying to use R to plot TSS binding site location vs log-likelihood values. I believe this falls under the purview of "Bioinformatics". Hence posted here.
It'd help if you showed an example of what you're trying to do. I assume you're trying to just plot average lines in different colors, in which case ggplot2 makes this quite simple (not that you can't use the base graphics, they're just less convenient).
Average log-likehood ratios (0.1, 0.3, 0.5 etc) on Y-axis vs.distance to TSS binding site (in bp ie -5000 -2500, 0, +2500, +5000) lines on X axis. 4 lines for the 4 tss1, 2, 3, 4 files. each of the 4 files has log-likehood ration column and distance to TSS column. So I guess yes, 4 lines in diff colors.