graph_from_aas {surfaltr} | R Documentation

## Create a plot showing membrane locations of each protein based on user provided amino acid sequences

### 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 amino acid sequences 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_aas(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 graphical 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_aas(
            system.file("extdata", "crb1_example.csv", package = "surfaltr"),
            "mouse", "combo", 1, "tmhmm", 4, -300, TRUE
        )
    }

[Package surfaltr version 1.0.0 Index]