Keep genes without mutations using waterfall

[Tato14]

Hi!

I am working with targeted panel sequencing and I would like to know if I could keep all the genes from the targeted panel, although some of them does not have any mutation reported. I tried to add empty rows with the gene names in the working data frame but does not solve the problem.

Any suggestions? Thanks!

[zlskidmore]

Hi @Tato14

This is not currently something GenVisR can do, but it shouldn't be hard to implement. I should have a patch as soon as today, but more realistically tuesday or wednesday CST

[malachig]

Thanks for the suggestion @Tato14. This is a good use case that probably quite a few people would find useful.

[Tato14]

Happy to help @malachig :)

[zlskidmore]

Hi @Tato14

I've just pushed a commit that adds this functionality. Note that the functionality is only present on the newer Waterfall() function (capital W). Here is an example:

library(data.table)
library(GenVisR)

# create example data for main plot
test <- data.table("sample"=c(rep("test1", 5), rep("test2", 5)), "gene"=c(rep("egfr", 2), rep("rb1", 3), rep("pik3ca", 3), rep("apc", 2)), "mutation"=c(rep("missense", 2), rep("nonsense", 2), "frameshift", rep("missense", 5)))

# create mutation hierarchy
test2 <- data.table("mutation"=c("missense", "nonsense", "frameshift"), "color"=c("red", "green", "blue"))

# run the new Waterfall function and save the result
out <- Waterfall(test, genes=c("not_here_1", "not_here_2"),
 mutationHierarchy=test2,
recurrence=.01)

# draw the output
drawPlot(out)

you can install this version of GenVisR with the devtools package devtools::install_github("griffithlab/GenVisR") the version installed should be 1.13.4

I still need to complete vignettes for these newer GenVisR* functions but just give it a data.table or data.frame and you should be fine, the Rdocumentation is mostly complete and can be viewed with ?Waterfall

Let me know if you have any issues

[Tato14]

It works great! Thanks @zlskidmore !

[zlskidmore]

Awesome!, if you run into any issues feel free to reopen!