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] "/tmp/RtmpEhstEg/Rinst2886b054afd/seqcombo/examples/GVariation/A.Mont.fas"  
## [2] "/tmp/RtmpEhstEg/Rinst2886b054afd/seqcombo/examples/GVariation/B.Oz.fas"    
## [3] "/tmp/RtmpEhstEg/Rinst2886b054afd/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 3.4.2 (2017-09-28)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.3 LTS
## 
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.6-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.6-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] igraph_1.1.2    ggplot2_2.2.1   emojifont_0.5.0 tibble_1.3.4   
## [5] seqcombo_1.0.0 
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.13        compiler_3.4.2      plyr_1.8.4         
##  [4] XVector_0.18.0      bindr_0.1           sysfonts_0.7.1     
##  [7] prettydoc_0.2.0     tools_3.4.2         zlibbioc_1.24.0    
## [10] digest_0.6.12       evaluate_0.10.1     gtable_0.2.0       
## [13] pkgconfig_2.0.1     rlang_0.1.2         rvcheck_0.0.9      
## [16] yaml_2.1.14         parallel_3.4.2      proto_1.0.0        
## [19] bindrcpp_0.2        showtextdb_2.0      stringr_1.2.0      
## [22] dplyr_0.7.4         knitr_1.17          Biostrings_2.46.0  
## [25] S4Vectors_0.16.0    IRanges_2.12.0      stats4_3.4.2       
## [28] rprojroot_1.2       grid_3.4.2          cowplot_0.8.0      
## [31] glue_1.2.0          R6_2.2.2            rmarkdown_1.6      
## [34] magrittr_1.5        backports_1.1.1     scales_0.5.0       
## [37] htmltools_0.3.6     BiocGenerics_0.24.0 showtext_0.5       
## [40] assertthat_0.2.0    colorspace_1.3-2    labeling_0.3       
## [43] stringi_1.1.5       lazyeval_0.2.1      munsell_0.4.3