Package: Plasmidprofiler 0.1.6
Plasmidprofiler: Visualization of Plasmid Profile Results
Contains functions developed to combine the results of querying a plasmid database using short-read sequence typing with the results of a blast analysis against the query results.
Authors:
Plasmidprofiler_0.1.6.tar.gz
Plasmidprofiler_0.1.6.zip(r-4.5)Plasmidprofiler_0.1.6.zip(r-4.4)Plasmidprofiler_0.1.6.zip(r-4.3)
Plasmidprofiler_0.1.6.tgz(r-4.4-any)Plasmidprofiler_0.1.6.tgz(r-4.3-any)
Plasmidprofiler_0.1.6.tar.gz(r-4.5-noble)Plasmidprofiler_0.1.6.tar.gz(r-4.4-noble)
Plasmidprofiler_0.1.6.tgz(r-4.4-emscripten)Plasmidprofiler_0.1.6.tgz(r-4.3-emscripten)
Plasmidprofiler.pdf |Plasmidprofiler.html✨
Plasmidprofiler/json (API)
| # Install 'Plasmidprofiler' in R: |
| install.packages('Plasmidprofiler', repos = c('https://thezetner.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 8 years agofrom:5d76478994. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 03 2024 |
| R-4.5-win | OK | Sep 03 2024 |
| R-4.5-linux | OK | Sep 03 2024 |
| R-4.4-win | OK | Sep 03 2024 |
| R-4.4-mac | OK | Sep 03 2024 |
| R-4.3-win | OK | Sep 03 2024 |
| R-4.3-mac | OK | Sep 03 2024 |
Exports:amr_positivesamr_presenceblast_parsercombine_resultscreate_grobcreate_plotlydefine_coloursfile_cachermainminmaxnormalizeorder_reportplot_heatmapread_blastread_srst2save_filessubsamplertree_makerzetner_score
Dependencies:apeaskpassbase64encbslibcachemclicolorspacecpp11crosstalkcurldata.tabledigestdplyrevaluatefansifarverfastmapfontawesomefsgdatagenericsggdendroggplot2gluegridExtragtablegtoolshighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplotlyplyrpromisespurrrR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownsassscalesstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Identify Antimicrobial Resistance Positive Plasmids from Blast Results | amr_positives |
| Adds the AMR_gene column to report | amr_presence |
| Blast Results Parser Function | blast_parser |
| Example Table of Blast Results | blastdata |
| Combines SRST2 and Blast results into a single dataframe | combine_results |
| Create Heatmap Graphical Object | create_grob |
| Create Plotly Object | create_plotly |
| Defining Colours Based on a Column of Data | define_colours |
| Filecacher | file_cacher |
| Main: Run everything | main |
| Minmax | minmax |
| Normalize | normalize |
| Order the Report | order_report |
| Create GGPLOT Heatmap | plot_heatmap |
| Blast file import function | read_blast |
| SRST2 file import function | read_srst2 |
| Example Complete Report after the following steps. Blast data from attached blastdata table SRST2 data from attached srst2data table | report |
| Save Files | save_files |
| Example Table of SRST2 Results | srst2data |
| Subsetting Results | subsampler |
| Create Dendrogram Based on Plasmid Content | tree_maker |
| Adds the Zetner Score column to report | zetner_score |
