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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
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_orderparam when filetype is Custom, you can just use unique(tmp$variant_class) for that for now