Waterfall failing with custom file: Error in `colnames<-`(`*tmp*`, value = c("sample", "gene", "trv_type")) : attempt to set 'colnames' on an object with less than two dimensions
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Entering edit mode
Jeni • 0
@jeni-23673
Last seen 8 months ago

Hi!

I am trying to get a plot of genes mutated per sample with waterfall() function from GenVisR package.

These are the first rows of my data frame, including their colnames:

   chr     start       end      REF   ALT     sample        gene     variant_class
   18    752225      752225      A     T      patient_2A   geneA     missense_variant
   2   291000000   291000000     T     C      patient_3A   geneB     missense_variant
   1      38270       38270      C     A      patient_2B   geneD     missense_variant
   1   56729899     56729899     A     T      patient_2B   geneC     missense_variant
   1    6824432      6824432     C     T      patient_3B   geneA     missense_variant
   14  12833945     12833945     C     T      patient_3B   geneF     missense_variant

When running the command:

waterfall(allVariants_toPlot, fileType = 'Custom')

I get the following error:

Checking if input is properly formatted...
Detected "Custom" file_type flag, looking for correct column names...
 Error in `colnames<-`(`*tmp*`, value = c("sample", "gene", "trv_type")) : 
  attempt to set 'colnames' on an object with less than two dimensions

How can I solve this?

This is my sessionInfo

R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] GenVisR_1.20.0              maftools_2.4.12             xlsx_0.6.4.2                enrichR_2.1                 data.table_1.13.0          
 [6] eply_0.1.2                  magrittr_1.5                stringr_1.4.0               purrr_0.3.4                 dplyr_1.0.2                
[11] VariantAnnotation_1.34.0    Rsamtools_2.4.0             SummarizedExperiment_1.18.2 DelayedArray_0.14.1         matrixStats_0.57.0         
[16] Biobase_2.48.0              GenomicRanges_1.40.0        GenomeInfoDb_1.24.2         Biostrings_2.56.0           XVector_0.28.0             
[21] IRanges_2.22.2              S4Vectors_0.26.1            BiocGenerics_0.34.0        

loaded via a namespace (and not attached):
 [1] viridis_0.5.1            httr_1.4.2               viridisLite_0.3.0        bit64_4.0.5              splines_4.0.2            gtools_3.8.2            
 [7] assertthat_0.2.1         askpass_1.1              BiocManager_1.30.10      BiocFileCache_1.12.1     blob_1.2.1               xlsxjars_0.6.1          
[13] BSgenome_1.56.0          GenomeInfoDbData_1.2.3   progress_1.2.2           pillar_1.4.6             RSQLite_2.2.1            lattice_0.20-41         
[19] glue_1.4.2               digest_0.6.25            RColorBrewer_1.1-2       colorspace_1.4-1         plyr_1.8.6               FField_0.1.0            
[25] Matrix_1.2-18            XML_3.99-0.5             pkgconfig_2.0.3          biomaRt_2.44.1           zlibbioc_1.34.0          scales_1.1.1            
[31] BiocParallel_1.22.0      tibble_3.0.3             openssl_1.4.3            generics_0.0.2           ggplot2_3.3.2            ellipsis_0.3.1          
[37] GenomicFeatures_1.40.1   survival_3.2-7           crayon_1.3.4             memoise_1.1.0            tools_4.0.2              prettyunits_1.1.1       
[43] hms_0.5.3                lifecycle_0.2.0          munsell_0.5.0            AnnotationDbi_1.50.3     compiler_4.0.2           rlang_0.4.7             
[49] grid_4.0.2               RCurl_1.98-1.2           rstudioapi_0.11          rjson_0.2.20             rappdirs_0.3.1           bitops_1.0-6            
[55] gtable_0.3.0             DBI_1.1.0                curl_4.3                 R6_2.4.1                 gridExtra_2.3            GenomicAlignments_1.24.0
[61] rtracklayer_1.48.0       bit_4.0.4                rJava_0.9-13             stringi_1.5.3            Rcpp_1.0.5               vctrs_0.3.4             
[67] dbplyr_1.4.4             tidyselect_1.1.0
variants waterfall GenVisR • 164 views
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Entering edit mode

I'm having trouble reproducing this, what does str(allVariants_toPlot) say, is anything a list instead of a vector? Are you comfortable using R's debugging tools? I can tell you exactly where this is failing, but I cannot say why it is failing there without being able to reproduce this.

As a quick test can you run this through, brcaMAF is automatically loaded with GenVisR

tmp <- head(brcaMAF[,c("Tumor_Sample_Barcode", "Hugo_Symbol", "Variant_Classification")]) colnames(tmp) <- c("sample", "gene", "variant_class")

Note you also need to supply a variant_class_order param when filetype is Custom, you can just use unique(tmp$variant_class) for that for now

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