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Plotting GO annotation results

Hi all friends,

I used TRAPID for GO annotation of a plant de novo assembled transcriptome, the output is a large text file (about 16 MB) like below:

 ab29703    GO:0019219
ab29703 GO:0009059
ab29707 GO:0044446
ab29707 GO:0006810
ab29707 GO:0044424
Contig6742  GO:0044260
Contig6742  GO:0003824
Contig6742  GO:0016772

I plan to use WEGO (enter link description here) for categorizing and plotting the GO annotation results, but the input of WEGO is something like:

ab29703 GO:0019219  GO:0009059
ab29707 GO:0044446  GO:0006810  GO:0044424
Contig6742  GO:0044260  GO:0003824  GO:0016772

Could you please help me out how I can change the original output format to accept by WEGO? Any comments and suggestion for using other tools for plant GO annotation and plotting would be highly appreciated.

go annotation transcriptome plotting
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updated by ivivek_ngs ivivek_ngs • written by seta seta

2 answers

Hi Seta,

I had a kinda similar question on the bioconductor site https://support.bioconductor.org/p/77134/

You can use dplyr in R to get what you want.

Good luck!

Ben

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written by Benn Benn

Thanks for your reply. However, my question differed with yours; actually, I would like to have all GO term from one gene in every row of a text file. Please let me know if you have any suggestion.

Best

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written by seta seta

Yes, but the principle is the same right? Switch the genes with the go terms?

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written by Benn Benn

Sorry, I am not much familiar with R. Could you please put the appropriate command for using "dplyr" to get GO term from one gene in every row of a text file?

Thanks for your help,

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written by seta seta

Assuming you have a tab-del txt file named "exampl.txt"

library(dplyr)

df<-read.table("exampl.txt")

reshaped <- group_by(df, V1) %>% summarise(GO = paste(V2, collapse = "\t"))

write.table(reshaped, "reshaped.txt", sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE)
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written by Benn Benn

Thank you very much b.nota. I try it.

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written by seta seta

I tried your suggested command, it worked well.

again thanks

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written by seta seta

Are you only restricted to using WEGO? you can simply do it yourself as well using R or as @b.nota said. In that case you will have to write a small script to count the number of GO terms each gene is having and then print that matrix and make any plots per row for those those genes , wither a barplot or even a heatmap.

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written by ivivek_ngs ivivek_ngs

Thanks, vchris_ngs. No, I'm not restricted to use WEGO. Regarding your comment, I also have another txt file with below information in every row:

go  description     num_transcripts transcripts

GO:0000033  alpha-1,3-mannosyltransferase activity  3   Contig12621 Contig15208 ab76639

In fact, there is the number of transcript with a given GO term in this file. however, I don't know how to use it for plotting.

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written by seta seta

Now you have it , for each gene the corresponding GO terms. as you put your example.

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written by ivivek_ngs ivivek_ngs

No, I have a given GO term for multiple genes, while I want to have all corresponding GO terms for each gene in every row of a txt file.

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written by seta seta

Thats what I wrote that b.nota has already shown it, sorry I did not mention his name in my comment.

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written by ivivek_ngs ivivek_ngs

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