graph_from_ids: Create a plot showing membrane locations of each protein...

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

Create a plot showing membrane locations of each protein based on transcript IDs

Description

This function creates a ggplot figure showing the differences in membrane location and length between primary and alternative transcripts from the same gene. This process is performed based on input data containing the gene names and transcript IDs of the proteins in question. 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

graph_from_ids(data_file, organism = "human", rank = "length",
n_prts = 20, mode = "phobius", size_txt = 2, space_left = -400, temp = FALSE,
tmhmm_folder_name = NULL)

Arguments

data_file	Path to the input file
organism	String indicating if the transcripts are from a human or a mouse
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.
mode	String detailing whether TMHMM or Phobius should be used to predict transmembrane regions. Input values include "phobius" or "tmhmm".
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.
temp	Boolean indicating if the fasta file should be deleted after the function finishes running or not. Recommended to always be set to FALSE.
tmhmm_folder_name	Full path to folder containing installed TMHMM 2.0 software. This value should end in TMHMM2.0c and needs to be provided if the mode used is TMHMM.

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)) {
    graph_from_ids(
        system.file("extdata", "hpa_example.csv", package = "surfaltr"),
        "human", "length", 1, "tmhmm", 5, -300, TRUE
    )
}

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