Sequence difference plot

Here we use the data published in Potato Research(Chang et al. 2015) as an example.

## [1] "/private/tmp/RtmpRlvbIV/Rinst9fcf2ddd913b/seqcombo/examples/GVariation/A.Mont.fas"  
## [2] "/private/tmp/RtmpRlvbIV/Rinst9fcf2ddd913b/seqcombo/examples/GVariation/B.Oz.fas"    
## [3] "/private/tmp/RtmpRlvbIV/Rinst9fcf2ddd913b/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.

## 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:

We can parse several files and visualize them simultaneously.

Sequence similarity plot

Session info

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

## R version 3.5.2 Patched (2018-12-20 r75875)
## 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/3.5/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] C/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  methods   base     
## 
## other attached packages:
## [1] igraph_1.2.2    ggplot2_3.1.0   emojifont_0.5.2 tibble_1.4.2   
## [5] seqcombo_1.4.1 
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.0          compiler_3.5.2      pillar_1.3.1       
##  [4] plyr_1.8.4          XVector_0.22.0      bindr_0.1.1        
##  [7] sysfonts_0.8        prettydoc_0.2.1     tools_3.5.2        
## [10] zlibbioc_1.28.0     digest_0.6.18       evaluate_0.12      
## [13] gtable_0.2.0        pkgconfig_2.0.2     rlang_0.3.0.1      
## [16] rvcheck_0.1.3       yaml_2.2.0          parallel_3.5.2     
## [19] xfun_0.4            proto_1.0.0         bindrcpp_0.2.2     
## [22] withr_2.1.2         showtextdb_2.0      stringr_1.3.1      
## [25] dplyr_0.7.8         knitr_1.21          Biostrings_2.50.1  
## [28] S4Vectors_0.20.1    IRanges_2.16.0      tidyselect_0.2.5   
## [31] stats4_3.5.2        grid_3.5.2          cowplot_0.9.3      
## [34] glue_1.3.0          R6_2.3.0            rmarkdown_1.11     
## [37] purrr_0.2.5         magrittr_1.5        scales_1.0.0       
## [40] htmltools_0.3.6     BiocGenerics_0.28.0 showtext_0.5-1     
## [43] assertthat_0.2.0    colorspace_1.3-2    labeling_0.3       
## [46] stringi_1.2.4       lazyeval_0.2.1      munsell_0.5.0      
## [49] crayon_1.3.4

References

Chang, Fei, Fangluan Gao, Jianguo Shen, Wenchao Zou, Shuang Zhao, and Jiasui Zhan. 2015. “Complete Genome Analysis of a PVYN-Wi Recombinant Isolate from Solanum Tuberosum in China.” Potato Research 58 (4):377–89. https://doi.org/10.1007/s11540-015-9307-3.