plot_isoforms: Create a plot showing where each amino acid is located within...

In EliLillyCo/surfaltr: Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr

Create a plot showing where each amino acid is located within the cell for each primary transcript compared to each alternative transcript

Description

This function creates a ggplot figure showing the differences in membrane location and length between primary and alternative transcripts from the same gene. Transcripts derived from the same gene are grouped together to facilitate easy interpretation. The y axis lists the gene name and transcript ID for each transcript and the x axis lists the length in amino acids. Each fill color corresponds to a membrane location and either principal or alternative isoform.

Usage

plot_isoforms(topo, AA_seq, rank = "length", n_prts = 20,
size_txt = 2, space_left = -400)

Arguments

topo	Outputted data frame from the run_phobius or get_tmhmm function showing membrane locations of amino acids and transcript IDs
AA_seq	A data frame outputted by the get_pairs function containing the gene names, transcript IDs, APPRIS annotations, and protein sequences for each transcript.
rank	String indicating which method to use to rank proteins in graphicl output. Options include "length", "TM", and "combo".
n_prts	Integer value indicating the number of genes that should be displayed on the graphical output. Default value is 20.
size_txt	Integer value specifying the size of the row labels. Default size is 2.
space_left	Integer value specifying how far left the graph should extend.

Value

A ggplot figure showing the protein locations for each part of the surface protein for each alternative and primary transcripts.

Examples

tmhmm_folder_name <- "~/TMHMM2.0c"
if (check_tmhmm_install(tmhmm_folder_name)) {
    currwd <- getwd()
    AA_seq <- get_pairs(system.file("extdata", "crb1_example.csv",
        package = "surfaltr"
    ), TRUE, "mouse", TRUE)
    topo <- run_phobius(AA_seq, paste(getwd(), "/AA.fasta", sep = ""))
    plot_isoforms(topo, AA_seq, "combo", 15, 3, -400)
    setwd(currwd)
}

EliLillyCo/surfaltr documentation built on May 3, 2022, 10:12 a.m.