Question: legChrom = NA doesn't hide legend
gravatar for jordi.planells
4 months ago by
jordi.planells0 wrote:

Hi all! I am using the package chromPlot but I'm having some problems with the legend placement. According to chromPlot manual:

(...)two options: 1. setting the legChrom argument to an arbitrary chromosome name 2. setting the legChrom to NA to omit plotting a legend.

First showing the structure of my data:

> head(data)
  Chrom    Start      End         Group
1 chr2L  1573892  1573953  SimpleRepeat
2 chr2L  1589915  1589962 LowComplexity
3 chr2L  1596249  1596279  SimpleRepeat
4 chr2L 14803935 14804210           LTR
5  chrX    50787    55026          LINE
6  chrX    57732    63810          LINE

Here's my code:

chromPlot(gaps = gap_file, bands = data, title = "My title", legChrom = NA)

Here's my sessioninfo()

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=sv_SE.UTF-8       
 [7] LC_PAPER=sv_SE.UTF-8       LC_NAME=C                  LC_ADDRESS=C              

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

other attached packages:
[1] chromPlot_1.12.0     GenomicRanges_1.36.0 GenomeInfoDb_1.20.0  IRanges_2.18.1      
[5] S4Vectors_0.22.0     BiocGenerics_0.30.0  biomaRt_2.40.0       dplyr_0.8.1         

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1             XVector_0.24.0         pillar_1.4.1          
 [4] compiler_3.6.0         zlibbioc_1.30.0        prettyunits_1.0.2     
 [7] bitops_1.0-6           tools_3.6.0            progress_1.2.2        
[10] digest_0.6.19          bit_1.1-14             RSQLite_2.1.1         
[13] memoise_1.1.0          tibble_2.1.3           pkgconfig_2.0.2       
[16] rlang_0.4.0            DBI_1.0.0              rstudioapi_0.10       
[19] xfun_0.8               GenomeInfoDbData_1.2.1 httr_1.4.0            
[22] stringr_1.4.0          knitr_1.23             hms_0.4.2             
[25] bit64_0.9-7            tidyselect_0.2.5       glue_1.3.1            
[28] Biobase_2.44.0         R6_2.4.0               AnnotationDbi_1.46.0  
[31] XML_3.98-1.20          purrr_0.3.2            blob_1.1.1            
[34] magrittr_1.5           assertthat_0.2.1       stringi_1.4.3         
[37] RCurl_1.95-4.12        crayon_1.3.4

And finally I attach the plot produced: enter image description here

Basically, I would like to either move the legend to the bottom of Y chromosome (ie: legChrom = "Y") or eliminate the legend (legChrom = NA) and add it after with legend(). However none of these options work and the legend lies in the same position always (possible bug?)

Thanks in advance for your help!


chromplot • 103 views
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