How to plot REVIGO r script

Question

[kissaj]

Hello,

I've used REVIGO to analyze my GO data and I'd like to plot it in r using the "r script". I do not understand how to do this. I have never used r and have no clue how to use it at all.

Can someone tell me (in a simple way) how to use the automagically generated r script from REVIGO?

Thanks,
Andor

Answer 1

[SES]

You need R installed (obviously), and once you have R open just change to the directory containing the script (with setwd()) and type:

source("REViGO.r")

You will likely have to open the script in text editor and uncomment the first line that starts with install.packages to install a required package (called "ggplot2") to do the plotting. Or, just open R and type install.packages("ggplot2",dep=t) followed by the source command above. That will bypass the editing step.

[kissaj]

Ok, got there - but then I get the following error:

source("REVIGO_BP100.r")
Error: Use scale_size_area instead.
  Note that the behavior of scale_size_area is slightly different:
  by default it makes the area proportional to the numeric value. (Defunct; last used in version 0.9.2)

Suggestions?

[SES]

That is due to the use of an outdated function in the ggplot2 package. Try to change 'scale_area' to 'scale_size_area'.

[kissaj]

Hi,

Yeah, I don't think they'll help out. I'll try, but, it's been my experience that the big drawback of free software is a complete lack of support after a tool has been developed and published.

My current "workaround" is to pull images from screen capture.

Regards,
Andor

[SES]

This is not an answer to the question, so please post this type of response as a comment. That makes it easier for others to find answers. Also, there's no reason to think they won't help if you haven't tried! If they weren't supporting the tool then the web service wouldn't be available.

[kissaj]

Sorry - didn't understand the difference...(between comment and answer)

[SES]

No worries, it just helps to follow the discussion when you respond directly to a comment rather than somewhere else.

[kissaj]

More issues

Scale for 'size' is already present. Adding another scale for 'size', which will replace the existing scale.
Scale for 'size' is already present. Adding another scale for 'size', which will replace the existing scale.
Error: Use 'theme' instead. (Defunct; last used in version 0.9.1)

[SES]

I could help with these messages, but I can't see your exact script so we could go back and forth like this for quite a while. Just email the authors and ask them to update the code, I'm sure they will help since this tool is published.

Answer 2

[Carin]

I know this is probably too late for you to use, but in case someone else has no experience with R and wants to plot the graph, Excel has a "Bubble Chart" that will give you want you need, though getting the different colours requires a bit of extra work. You just export the csv file and use the coordinates and plot size to draw the chart.