1- How can I simply download REVIGO scatter-plot and/or TreeMap as image (not .CSV or .r)?
2- I have found a Python script here (appreciate it's creator) and it goes well for it's the example but I can not use that for my own data.
of course it has some help as "# For actual data, use open('mydata.txt').read()" in this regard, but I could not figure out how I should change the script and where I should put my data as they are already online I the REVIGO site and my results are online, too.
Hi, @ Diwan and thanks, I have installed it and tried that but I received the following error:
Hi and thank you,
I works for sample#1 for me, but when I used my own data, the same error occurred:
As it works for the example, its difficult to understand the error message without further details. I can only guess. Based on the script, there is an assignment: vSize = "abslog10pvalue" Can you check if you get some results for : stuff$abslog10pvalue
In example #1, you get something like  22 5 300 26 10 25 113 10...........
you mean I should use "
vSize = "stuff$abslog10pvalue"" ?
I now understand, As I did not use pValue for my graph, the error occur,
So, I made "vSize = "abslog10pvalue"" as comment,
BUT new error has arose :
AND another try:
so, I guess I must make R realize that I am not using p values, but commenting the " vSize" is not working.
Good. So that is the source of error. The usual input is GO IDs and associated p-value. Since you don't have pvalue you are getting error where ever it is mentioned. You should comment that line in the script too. As you can see, the Rscript creates a dataframe called stuff with GO terms, pvalues etc and then pass it to treemap function. HTH
check ?treemap as tmPlot is deprecated. It says dataframe, index, and vsize are required parameters for treemap (also tmPlot) function.