Sequence difference plot

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

## [1] "/tmp/RtmpP5ZN8R/Rinst20c11953812158/seqcombo/examples/GVariation/A.Mont.fas"  
## [2] "/tmp/RtmpP5ZN8R/Rinst20c11953812158/seqcombo/examples/GVariation/B.Oz.fas"    
## [3] "/tmp/RtmpP5ZN8R/Rinst20c11953812158/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 4.1.0 (2021-05-18)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.13-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.13-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              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] ggplot2_3.3.5   emojifont_0.5.5 tibble_3.1.3    seqcombo_1.14.1
## 
## loaded via a namespace (and not attached):
##  [1] prettydoc_0.4.1        tidyselect_1.1.1       xfun_0.25             
##  [4] bslib_0.2.5.1          purrr_0.3.4            colorspace_2.0-2      
##  [7] vctrs_0.3.8            generics_0.1.0         htmltools_0.5.1.1     
## [10] stats4_4.1.0           yaml_2.2.1             utf8_1.2.2            
## [13] rlang_0.4.11           jquerylib_0.1.4        pillar_1.6.2          
## [16] withr_2.4.2            glue_1.4.2             DBI_1.1.1             
## [19] BiocGenerics_0.38.0    GenomeInfoDbData_1.2.6 lifecycle_1.0.0       
## [22] stringr_1.4.0          zlibbioc_1.38.0        Biostrings_2.60.2     
## [25] munsell_0.5.0          gtable_0.3.0           evaluate_0.14         
## [28] labeling_0.4.2         knitr_1.33             IRanges_2.26.0        
## [31] GenomeInfoDb_1.28.1    parallel_4.1.0         fansi_0.5.0           
## [34] highr_0.9              proto_1.0.0            scales_1.1.1          
## [37] showtext_0.9-4         S4Vectors_0.30.0       jsonlite_1.7.2        
## [40] XVector_0.32.0         sysfonts_0.8.5         farver_2.1.0          
## [43] digest_0.6.27          stringi_1.7.3          showtextdb_3.0        
## [46] dplyr_1.0.7            cowplot_1.1.1          grid_4.1.0            
## [49] tools_4.1.0            bitops_1.0-7           yulab.utils_0.0.2     
## [52] magrittr_2.0.1         sass_0.4.0             RCurl_1.98-1.4        
## [55] crayon_1.4.1           pkgconfig_2.0.3        ellipsis_0.3.2        
## [58] assertthat_0.2.1       rmarkdown_2.10         R6_2.5.1              
## [61] igraph_1.2.6           compiler_4.1.0

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.