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Question: Gviz cannot make gene region track
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gravatar for iaingallagher
4 months ago by
iaingallagher0 wrote:

Hi

In the script below I'm trying to plot a single gene using Gvis. On trying to create the gene track I get the following error:

Error in chromosome[1] : object of type 'closure' is not subsettable

Can anyone shed any light on this?

Code follows:

# plot tfbs in IS core correlating genes
library(Gviz)
library(GenomicRanges)
library(biomaRt)

rm(list=ls())

# gene syms
syms <- c("MCCC1","PCYT2","ALDH6A1","DHTKD1","ECHDC3","SLC43A1")

# create GenomicFeatures for the genes using biomaRt
mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
gene_data <- getBM(attributes = c('chromosome_name', 'start_position', 'end_position', 'strand',  'ensembl_gene_id', 'ensembl_exon_id', 'ensembl_transcript_id', 'hgnc_symbol'), filters = 'hgnc_symbol', values = syms , mart = mart)
# change strand info to required labels ('-', '+')
gene_data$strand <- ifelse(gene_data$strand==-1, '-', '+')
gene_data$chromosome_name <- as.character(paste('chr', gene_data$chromosome_name, sep=''))

# create seqinfo object
chrs <- unique(gene_data$chromosome_name)
chr_lns <- c(107043718, 133797422, 198295559, 83257441, 135086622)
isC <- rep(FALSE, 5)
hum_gen <- rep('hg19', 5)
seq_info <- Seqinfo(seqnames=chrs, seqlengths=chr_lns, isCircular=isC, genome=hum_gen)

# make GRanges obj
gene_GR <- makeGRangesFromDataFrame(gene_data, seqinfo=seq_info, seqnames.field = 'chromosome_name', start.field = 'start_position', end.field = 'end_position', strand.field = 'strand', keep.extra.columns=TRUE)

# create tracks for first gene
# get info
gene1 <- gene_GR[gene_GR$hgnc_symbol==syms[1]]
gen <- 'hg19'
gene_track <- GeneRegionTrack(gene1, genome = gen, chromosome = seqnames, name = "Gene Model")
Error in chromosome[1] : object of type 'closure' is not subsettable

Thanks,

Iain

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] ensembldb_2.0.3                         AnnotationFilter_1.0.0                 
 [3] BiocInstaller_1.26.0                    TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [5] GenomicFeatures_1.28.4                  AnnotationDbi_1.38.1                   
 [7] Biobase_2.36.2                          biomaRt_2.32.1                         
 [9] BSgenome.Hsapiens.UCSC.hg19_1.4.0       BSgenome_1.44.0                        
[11] rtracklayer_1.36.4                      Biostrings_2.44.1                      
[13] XVector_0.16.0                          Gviz_1.20.0                            
[15] GenomicRanges_1.28.3                    GenomeInfoDb_1.12.2                    
[17] IRanges_2.10.2                          S4Vectors_0.14.3                       
[19] BiocGenerics_0.22.0                    

loaded via a namespace (and not attached):
 [1] httr_1.2.1                    bit64_0.9-7                   AnnotationHub_2.8.2          
 [4] splines_3.4.0                 shiny_1.0.3                   Formula_1.2-2                
 [7] interactiveDisplayBase_1.14.0 latticeExtra_0.6-28           blob_1.1.0                   
[10] GenomeInfoDbData_0.99.0       Rsamtools_1.28.0              yaml_2.1.14                  
[13] RSQLite_2.0                   backports_1.1.0               lattice_0.20-35              
[16] biovizBase_1.24.0             digest_0.6.12                 RColorBrewer_1.1-2           
[19] checkmate_1.8.3               colorspace_1.3-2              httpuv_1.3.5                 
[22] htmltools_0.3.6               Matrix_1.2-10                 plyr_1.8.4                   
[25] pkgconfig_2.0.1               XML_3.98-1.9                  zlibbioc_1.22.0              
[28] xtable_1.8-2                  scales_0.4.1                  BiocParallel_1.10.1          
[31] htmlTable_1.9                 tibble_1.3.3                  ggplot2_2.2.1                
[34] SummarizedExperiment_1.6.3    nnet_7.3-12                   lazyeval_0.2.0               
[37] mime_0.5                      survival_2.41-3               magrittr_1.5                 
[40] memoise_1.1.0                 foreign_0.8-69                tools_3.4.0                  
[43] data.table_1.10.4             matrixStats_0.52.2            stringr_1.2.0                
[46] munsell_0.4.3                 cluster_2.0.6                 DelayedArray_0.2.7           
[49] compiler_3.4.0                rlang_0.1.1                   RCurl_1.95-4.8               
[52] dichromat_2.0-0               VariantAnnotation_1.22.3      htmlwidgets_0.9              
[55] bitops_1.0-6                  base64enc_0.1-3               gtable_0.2.0                 
[58] curl_2.7                      DBI_0.7                       R6_2.2.2                     
[61] GenomicAlignments_1.12.1      gridExtra_2.2.1               knitr_1.16                   
[64] bit_1.1-12                    Hmisc_4.0-3                   ProtGenerics_1.8.0           
[67] stringi_1.1.5                 Rcpp_0.12.11                  rpart_4.1-11                 
[70] acepack_1.4.1           

 

ADD COMMENTlink modified 4 months ago • written 4 months ago by iaingallagher0

Fixed this. The problem was the use of

chromosome = seqnames

in the last line... seqnames being a function. Hey ho.

best,

i

ADD REPLYlink written 4 months ago by iaingallagher0
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