'Error: Insufficient values in manual scale.' with custom file type when 'mainDropMut=F'

[u9090]

Hi,

Using waterfall with a custom file type with 16 variant classes (from Annovar), I get the following error:

Checking if input is properly formatted...
Detected "Custom" file_type flag, looking for correct column names...
Calculating frequency of mutations...
setting mutation hierarchy...
Performing recurrence cutoff...
Error: Insufficient values in manual scale. 18 needed but only 16 provided.

This only occurs when mainDropMut=F.

Everything works fine when mainDropMut=T. But it also drops sample columns for which no genes are mutated.

[zlskidmore]

hmm strange, looking into this now. As a temporary work-around specifying a custom palette via mainPalette with 18 colors should resolve the issue until I can figure out what's going on.

[zlskidmore]

@lavv2 I'm having problems reproducing the error you are seeing, what version of GenVisR are you currently running?

Can you run this code without error?

tmp <- data.frame("sample"=as.character(c(1:20)), "gene"=as.character(c(1:20)), variant_class=as.character(c(1:19, "Silent")))

waterfall(tmp, fileType = "Custom", rmvSilent = T, mainDropMut = T, variant_class_order = as.character(tmp$variant_class))
waterfall(tmp, fileType = "Custom", rmvSilent = T, mainDropMut = F, variant_class_order = as.character(tmp$variant_class))

[u9090]

> tmp <- data.frame("sample"=as.character(c(1:20)), "gene"=as.character(c(1:20)), variant_class=as.character(c(1:19, "Silent")))
> 
> waterfall(tmp, fileType = "Custom", rmvSilent = T, mainDropMut = T, variant_class_order = as.character(tmp$variant_class))
Checking if input is properly formatted...
Detected "Custom" file_type flag, looking for correct column names...
Calculating frequency of mutations...
Removing silent mutations...
setting mutation hierarchy...
Error in waterfall_hierarchyTRV(data_frame, fileType, variant_class_order) : 
  Detected an invalid mutation type, valid values for Custom are: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, Silent
> 
> 
> 
> waterfall(tmp, fileType = "Custom", rmvSilent = T, mainDropMut = F, variant_class_order = as.character(tmp$variant_class))
Checking if input is properly formatted...
Detected "Custom" file_type flag, looking for correct column names...
Calculating frequency of mutations...
Removing silent mutations...
setting mutation hierarchy...
Error in waterfall_hierarchyTRV(data_frame, fileType, variant_class_order) : 
  Detected an invalid mutation type, valid values for Custom are: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, Silent

Installed the last version available from Bioconductor 2 weeks ago

> sessionInfo()
> R version 3.3.1 (2016-06-21)
> Platform: x86_64-pc-linux-gnu (64-bit)
> 
> locale:
> [1] C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] ggplot2_2.2.1 GenVisR_1.4.1
> 
> loaded via a namespace (and not attached):
>  [1] Rcpp_0.12.9                plyr_1.8.4                
>  [3] GenomeInfoDb_1.10.3        XVector_0.14.0            
>  [5] viridis_0.3.4              GenomicFeatures_1.26.3    
>  [7] bitops_1.0-6               tools_3.3.1               
>  [9] zlibbioc_1.20.0            biomaRt_2.30.0            
> [11] digest_0.6.12              RSQLite_1.1-2             
> [13] memoise_1.0.0              tibble_1.2                
> [15] gtable_0.2.0               lattice_0.20-34           
> [17] Matrix_1.2-8               DBI_0.5-1                 
> [19] parallel_3.3.1             gridExtra_2.2.1           
> [21] stringr_1.1.0              rtracklayer_1.34.2        
> [23] Biostrings_2.42.1          S4Vectors_0.12.1          
> [25] gtools_3.5.0               IRanges_2.8.1             
> [27] stats4_3.3.1               grid_3.3.1                
> [29] FField_0.1.0               Biobase_2.34.0            
> [31] AnnotationDbi_1.36.2       XML_3.98-1.5              
> [33] BiocParallel_1.8.1         magrittr_1.5              
> [35] reshape2_1.4.1             scales_0.4.1              
> [37] Rsamtools_1.26.1           BiocGenerics_0.20.0       
> [39] GenomicRanges_1.26.3       GenomicAlignments_1.10.0  
> [41] assertthat_0.1             SummarizedExperiment_1.4.0
> [43] colorspace_1.3-2           labeling_0.3              
> [45] stringi_1.1.2              RCurl_1.95-4.8            
> [47] lazyeval_0.2.0             munsell_0.4.3    

[zlskidmore]

installing the latest development version might fix the issue, you can do that with the following code. It will certainly fix the issue you ran into when running the code above. I will continue looking into this

library(devtools)
install_github("griffithlab/GenVisR")

[zlskidmore]

this should not be an issue anymore when using the updated Waterfall() function, closing