Sequence difference plot

Here we use the data published in Potato Research¹ as an example.

fas <- list.files(system.file("examples","GVariation", package="seqcombo"),
                  pattern="fas", full.names=TRUE)
fas

## [1] "/Library/R/library/seqcombo/examples/GVariation/A.Mont.fas"  
## [2] "/Library/R/library/seqcombo/examples/GVariation/B.Oz.fas"    
## [3] "/Library/R/library/seqcombo/examples/GVariation/C.Wilga5.fas"

The input fasta file should contains two aligned sequences. User need to specify which sequence (1 or 2, 1 by default) as reference. The seqdiff function will parse the fasta file and calculate the nucleotide differences by comparing the non-reference one to reference.

x1 <- seqdiff(fas[1], reference=1)
x1

## sequence differences of Mont and CF_YL21 
## 1181 sites differ:
##   A   C   G   T 
## 286 315 301 279

We can visualize the differences by plot method:

plot(x1)

We can parse several files and visualize them simultaneously.

x <- lapply(fas, seqdiff)
plts <- lapply(x, plot)
plot_grid(plotlist=plts, ncol=1, labels=LETTERS[1:3])

Sequence similarity plot

fas <- system.file("examples/GVariation/sample_alignment.fa", package="seqcombo")
simplot(fas, 'CF_YL21')

Session info

Here is the output of sessionInfo() on the system on which this document was compiled:

## R version 3.4.1 (2017-06-30)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: OS X El Capitan 10.11.6
## 
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] stats     graphics  grDevices utils     datasets  base     
## 
## other attached packages:
## [1] seqcombo_0.99.4
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.12        compiler_3.4.1      plyr_1.8.4         
##  [4] XVector_0.16.0      bindr_0.1           methods_3.4.1      
##  [7] prettydoc_0.2.0     tools_3.4.1         zlibbioc_1.22.0    
## [10] digest_0.6.12       evaluate_0.10.1     tibble_1.3.3       
## [13] gtable_0.2.0        pkgconfig_2.0.1     rlang_0.1.1.9000   
## [16] igraph_1.1.2        rvcheck_0.0.9       yaml_2.1.14        
## [19] parallel_3.4.1      bindrcpp_0.2        stringr_1.2.0      
## [22] dplyr_0.7.2         knitr_1.16          Biostrings_2.44.2  
## [25] S4Vectors_0.14.3    IRanges_2.10.2      stats4_3.4.1       
## [28] rprojroot_1.2       grid_3.4.1          cowplot_0.8.0      
## [31] glue_1.1.1          R6_2.2.2            rmarkdown_1.6      
## [34] ggplot2_2.2.1       magrittr_1.5        backports_1.1.0    
## [37] scales_0.4.1        htmltools_0.3.6     BiocGenerics_0.22.0
## [40] assertthat_0.2.0    colorspace_1.3-2    labeling_0.3       
## [43] stringi_1.1.5       lazyeval_0.2.0      munsell_0.4.3