Gene Locus Map Generator

Molly Gordon
07/17/2020

Rationale

  • Geneticist often need to draw out the linear structure of genes for research and publications
  • This is complicated to do by hand or powerpoint due to human-induced inaccuracies for estimating sizes and distances between genes
  • This also takes considerable amounts of time to get less than perfect drawings

For more details on the Gene Locus Map Generator, visit the README.md at https://github.com/mgordo34/Gene_Locus_Map/blob/gh-pages/README.md.

Need for fast & accurate tools to draw gene maps

An R package, gggenes, has been developed to make accurate gene loci maps that I have found particularly helpful for my own research. https://cran.r-project.org/web/packages/gggenes/vignettes/introduction-to-gggenes.html.

  • I sought to generate a tool to input gene information and rapidly generate these maps with the click of a button
  • This bypasses the need for external datasets and allows users to quickly generate a plethora of gene maps on a need to need basis
  • The code below shows how the gggenes package functions.
library(gggenes)
library(ggplot2)
library(dplyr)
test <- read.csv("https://raw.githubusercontent.com/mgordo34/Gene_Locus_Map/gh-pages/test.csv")
 a <- test %>%

            ggplot(aes(xmin = Start, xmax = End, y = molecule, fill = Gene, forward=strand, label=Gene)) +
            geom_gene_arrow() + 
            geom_gene_label() + 
            facet_wrap(~ molecule, scales = "free", ncol = 1) +
            scale_fill_brewer(palette = "Set3") +
            theme_genes() + theme(legend.position="top", text = element_text(size=20), legend.title = element_blank(), axis.title = element_blank())

Necessary inputs for the "Gene Locus Map Generator"

  • Name of your project
  • Two genes occuring consecutively in any genome (i.e. human, mouse, yeast)
  • Chromosomal location of each gene
  • Orientation of each gene (i.e. expressed from forward or reverse strand)

The following table is some hypothetical data that can be used to generate a successful gene locus map for a convergent gene pair in budding yeast. Below the table is how the resulting gene locus map will look for this gene pair. 

  molecule  Gene Start End strand
1 Genome 1 CTF13     1 100      1
2 Genome 1  SNO1   120 190     -1

plot of chunk unnamed-chunk-2

Future Directions for "Gene Locus Map Generator"

Currently, the “Gene Locus Map Generator” is limited to displaying only a pair of genes. We would like to expand the “Gene Locus Map Generator” with the following improvements following this initial prototype:

  • Allow users to select the number of genes to display on a single locus (up to at least 5 genes)
  • Allow users to generate maps including multiple stacked molecules to display many loci from different protions of the genome, or even from different genomes comparing across species.