a R function part to visualizae the genes coming from the genome alignment. it adds the stranded information with in the R function so that it makes easier for the visualizer to analyze the genes. You can find the support for the multiple genes and the different ones in the evoseq evoseq.
- This is a part of the evoseq R package due for release next week. However you can use the function as a separate one.
- the sample figure is present and the sample file also.
- vectorized function so faster.
- run the function as
genevisualize <- function(genomealigned, annotationlevel)
# where genomealigned is the gff file
# annotationlevel = mRNA
# store the output as a list
output <- genevisualize(sample.gff, "mRNA")
- plot the genes as
library(ggplot2)
library(gggenes)
ggplot(output, aes(xmin = start, xmax = end, y = molecule, fill = gene)) +
geom_gene_arrow() +
facet_wrap(~ molecule, scales = "free", ncol = 1) +
scale_fill_brewer(palette = "Set3")
- adding a new variable declaration which allows you to change the ids of the specific molecules.
Gaurav
Academic Staff Member
Bioinformatics
Institute for Biochemistry and Biology
University of Potsdam
Potsdam,Germany