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BIMIB-DISCo / TRONCO

Repository of the TRanslational ONCOlogy library, which includes various algorithms (such as CAPRESE and CAPRI) and the Pipeline for Cancer Inference (PICNIC).
https://bimib-disco.github.io/TRONCO
GNU General Public License v3.0
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Error when trying to create a circos plot #107

Closed Tato14 closed 6 years ago

Tato14 commented 6 years ago

Hi!

I am trying to use the tronco.pattern.plot with some MAF data. I get the following error:

Error in matrix(unlist(value, recursive = FALSE, use.names = FALSE), nrow = nr, : 'data' must be of a vector type, was 'NULL'

Any thoughs? Thanks!

danro9685 commented 6 years ago

Dear @Tato14,

is seems that there is some missing/empty element in the list of patters. So I guess there must be something wrong with the TRONCO object you are giving as input to the tronco.pattern.plot function.

For more details, we will need to take a look at the data you are using as inputs.

Best, Daniele

Tato14 commented 6 years ago

Hi @danro9685 ,

I am completely new with this kind of analysis so I'm quite sure that I forgot something :). Here's an example of the data that I'm working with.

SM_tumor_merged.maf.zip

Thank you!

danro9685 commented 6 years ago

Hi @Tato14,

the MAF looks apparently good. You imported it with the function import.MAF? I have tried to use the import.MAF and then run the tronco.pattern.plot and everything worked fine. Can you tell me exactly the commands you run to get the error?

Best, Daniele

Tato14 commented 6 years ago

Hi @danro9685,

Yes, I used the following commands: SMmerged3<- import.MAF("SM_tumor_merged.maf") tronco.pattern.plot(SMmerged3,mode = "circos")

Tato14 commented 6 years ago

Sorry, the tronco.pattern.plot was: tronco.pattern.plot(SMmerged3, to = "Missense_Mutation", mode = "circos")

danro9685 commented 6 years ago

Dear @Tato14,

in the "to" you need to put a gene name. Specifically one of the genes you have in the dataset. You can find the list of valid gene names with as.genes(SMmerged3).

Best, Daniele