OncoPrint in a Shiny app

[msquatrito]

Hi Zuguang,
I'm not sure this is a problem of your package (most probably not!), but I'm having issues with using the oncoPrint function inside a Shiny app.
Run the code below for an example

library(shiny)
runGist("84cdc8af0a2b3e219883")

and here is the code for it: https://gist.github.com/msquatrito/84cdc8af0a2b3e219883

I've no problems in plotting mutation data only, but I've noticed inconsistencies when I combine them with copy number alteration data. Some of the mutations disappear when you select multiple genes at the same time and then reappear if you remove some of them. I know, it's hard to understand it in this way, maybe if you would have time to test it yourself you could see what is the issue. Try to type EGFR PTEN TP53 ATRX, and then start to remove them one by one. I know that the mutations are there, because if I make the color transparent I can see them. I guess it might be a problem at the time when the multiple layers of the plot are called.

Most probably it is an issue of my code, on the way a create the matrix with the mutation and copy number data, but I was wondering if you could have any suggestion on how to solve it.

Thanks in advance!
Massimo

[jokergoo]

In line #83, you changed the order of functions in alter_fun_list. In your case, when you add the copy number layer, the order becomes:

[1] "background" "HETLOSS"    "MUT"        "GAIN"       "AMP"
[6] "HOMDEL"

which means 'GAIN' layer will overlap 'MUT' layer.

add:

# make a subset but still keep the original order
alt = intersect(names(alter_fun_list), alt)

just above line #83 will solve this problem.

[msquatrito]

YES!! it solved it!!
Thank you so much.
Best,
Massimo