| Title: | Visualizing Sequence Alignment by Generating Publication-Ready Plots |
|---|---|
| Description: | Providing publication-ready graphs for Multiple sequence alignment. Moreover, it provides a unique solution for visualizing the multiple sequence alignment without the need to do the alignment in each run which is a big limitation in other available packages. |
| Authors: | Mohamed Soudy [aut, cre] |
| Maintainer: | Mohamed Soudy <[email protected]> |
| License: | GPL-3 |
| Version: | 0.1 |
| Built: | 2024-11-02 04:12:50 UTC |
| Source: | https://github.com/mohmedsoudy/ggaligner |
Generating a plot for msa object of DNA or Protein sequence
ggaligner(alignment,start=1,end=10,color="Clustal",font="helvetical",label_font = 12)ggaligner(alignment,start=1,end=10,color="Clustal",font="helvetical",label_font = 12)
alignment |
alignment object returned from msa package |
start |
start position of the desired alignment region |
end |
end position of the desired alignment region |
color |
color scheme to use ex: Clustal, Chemistry_AA, Shapely_AA |
font |
font family to use ex: helvetical, TimesNewRoman |
label_font |
font size of sequence names |
An enhanced plot for the alignment using ggplot2 and ggmsa packages
Mohamed Soudy [email protected]
convert string that can be DNA or protein sequence to a character vector
Seqtochar(x)Seqtochar(x)
x |
a sequence of DNA or Protein |
this function is mainly used by ggaligner function to convert the input sequence to character vector
Mohamed Soudy [email protected]
Seqtochar("ATGACATAAT")Seqtochar("ATGACATAAT")