Package: drawProteins 1.32.0

Paul Brennan

drawProteins: Package to Draw Protein Schematics from Uniprot API output

This package draws protein schematics from Uniprot API output. From the JSON returned by the GET command, it creates a dataframe from the Uniprot Features API. This dataframe can then be used by geoms based on ggplot2 and base R to draw protein schematics.

Authors:Paul Brennan [aut, cre]

drawProteins_1.32.0.tar.gz
drawProteins_1.32.0.zip(r-4.7-any)drawProteins_1.32.0.zip(r-4.6-any)drawProteins_1.32.0.zip(r-4.5-any)
drawProteins_1.32.0.tgz(r-4.6-any)drawProteins_1.32.0.tgz(r-4.5-any)
drawProteins_1.32.0.tar.gz(r-4.7-any)drawProteins_1.32.0.tar.gz(r-4.6-any)
drawProteins_1.32.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
drawProteins/json (API)

# Install 'drawProteins' in R:
install.packages('drawProteins', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/brennanpincardiff/drawproteins/issues

Datasets:
  • five_rel_data - Dataframe features of 5 human NFkappaB proteins Uniprot on 1 Nov 2017
  • five_rel_list - Features of five human Rel A proteins
  • protein_json - Uniprot infor human Rel A protein in JSON format
  • rel_A_features - Features of human Rel A protein
  • rel_json - Human Rel A protein features in JSON format
  • tnfs_data - Dataframe features of 2 human TNF receptors from Uniprot on 3 Jan 2018

On BioConductor:drawProteins-1.33.0(bioc 3.24)drawProteins-1.32.0(bioc 3.23)

visualizationfunctionalpredictionproteomics

8.88 score 35 stars 1 packages 80 scripts 513 downloads 6 mentions 16 exports 46 dependencies

Last updated from:0ae1012395 (on RELEASE_3_23). Checks:1 WARNING, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING165
linux-devel-x86_64OK188
source / vignettesOK204
linux-release-x86_64OK184
macos-release-arm64OK115
macos-oldrel-arm64OK89
windows-develOK97
windows-releaseOK101
windows-oldrelOK98
wasm-releaseOK150

Exports:draw_canvasdraw_chainsdraw_domainsdraw_foldingdraw_motifdraw_phosphodraw_recept_domdraw_regionsdraw_repeatextract_feat_accextract_namesextract_transcriptsfeature_to_dataframeget_featuresparse_gffphospho_site_info

Dependencies:askpassbitbit64clicliprcpp11crayoncurldplyrfarvergenericsggplot2gluegtablehmshttrisobandjsonlitelabelinglifecyclemagrittrmimeopensslpillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerreadrrlangS7scalesstringistringrsystibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithr

Using extract_transcripts in drawProteins
Introducing extract_transcripts() in drawProteins | Making a new dataframe with each transcript separated | Session info
Rendered fromdrawProteins_extract_transcripts_BiocStyle.Rmdusingknitr::rmarkdown

Last update: 2019-01-30
Started: 2018-01-03

Using drawProteins
Overview of drawProteins | Getting the data from Uniprot | Turning Uniprot data into a dataframe | Draw the protein chains and domains | Checking the other features | Putting it all together | Adding titles to the plots | Drawing schematic for multiple proteins | Customising the draw functions | Session info
Rendered fromdrawProteins_BiocStyle.Rmdusingknitr::rmarkdown

Last update: 2019-01-30
Started: 2017-08-17

Readme and manuals

Help Manual

Help pageTopics
Create ggplot2 object with protein chains from feature databasedraw_canvas
Create ggplot2 object with protein chains from feature databasedraw_chains
Add protein domains to ggplot2 object.draw_domains
Add regions to ggplot object: alpha-helixes, beta-strands and turns.draw_folding
Add protein motifs sites to ggplot2 object.draw_motif
Add protein phosphorylation sites to ggplot2 object.draw_phospho
Add receptor domains to ggplot2 object.draw_recept_dom
Add protein region sites to ggplot2 object.draw_regions
Add protein repeats sites to ggplot2 object.draw_repeat
drawProteins.drawProteins
Create a dataframe of protein features from JSON object (List of 6)extract_feat_acc
Extract protein names into a listextract_names
Create a new dataframe of protein features from dataframe with multiple transcripts separated so that each transcript is drawn separtely with only the appropriate features.extract_transcripts
Create a dataframe of protein features from JSON objectfeature_to_dataframe
Dataframe features of 5 human NFkappaB proteins Uniprot on 1 Nov 2017five_rel_data
Features of five human Rel A proteinsfive_rel_list
GET features of protein(s) from UniProt APIget_features
Reformat file or url in gff format to allow to drawparse_gff
Create a dataframe of protein features from JSON objectphospho_site_info
Uniprot infor human Rel A protein in JSON formatprotein_json
Features of human Rel A proteinrel_A_features
Human Rel A protein features in JSON formatrel_json
Dataframe features of 2 human TNF receptors from Uniprot on 3 Jan 2018tnfs_data