The goal of AlphaPep is to visualize proteomic and peptidomic data on a structural level
# install.packages("devtools")
devtools::install_github("loganjohnson0/AlphaPep")
#> Skipping install of 'AlphaPep' from a github remote, the SHA1 (a9c9aaf2) has not changed since last install.
#> Use `force = TRUE` to force installationThis is a basic example which shows you how to solve a common problem:
library(AlphaPep)
AlphaPep::get_alphafold2(uniprot_id = "P02540")
#> No encoding supplied: defaulting to UTF-8.library(NGLVieweR)
library(tidyverse, quietly = TRUE)
#> ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
#> ✔ dplyr 1.1.2 ✔ readr 2.1.4
#> ✔ forcats 1.0.0 ✔ stringr 1.5.0
#> ✔ ggplot2 3.4.2 ✔ tibble 3.2.1
#> ✔ lubridate 1.9.2 ✔ tidyr 1.3.0
#> ✔ purrr 1.0.1
#> ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
#> ✖ dplyr::filter() masks stats::filter()
#> ✖ dplyr::lag() masks stats::lag()
#> ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
NGLVieweR::NGLVieweR(data = "AlphaFold_Structure.pdb") %>%
NGLVieweR::addRepresentation(type = "cartoon",
param = list(
name = "cartoon",
color = "residueindex")) %>%
NGLVieweR::stageParameters(backgroundColor = "black") %>%
NGLVieweR::setQuality("high") %>%
NGLVieweR::setFocus(0) %>%
NGLVieweR::setSpin(TRUE)
#> Warning in readLines(data): incomplete final line found on
#> 'AlphaFold_Structure.pdb'