From 588aeb2ae8d5b27b1a8a72415576a281eea4574e Mon Sep 17 00:00:00 2001 From: sdgamboa Date: Wed, 20 Mar 2024 13:59:15 -0400 Subject: [PATCH] update README. Move workflow to wiki --- DESCRIPTION | 2 +- README.md | 34 +- vignettes/Drawing.svg | 802 ----------------------------------------- vignettes/workflow.Rmd | 26 -- 4 files changed, 8 insertions(+), 856 deletions(-) delete mode 100644 vignettes/Drawing.svg delete mode 100644 vignettes/workflow.Rmd diff --git a/DESCRIPTION b/DESCRIPTION index d23c9266..f95e35f7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: bugphyzz Title: A harmonized data resource and software for enrichment analysis of microbial physiologies -Version: 0.0.1.7 +Version: 0.0.1.8 Authors@R: c( person( diff --git a/README.md b/README.md index 5cae29f4..98b825e7 100644 --- a/README.md +++ b/README.md @@ -9,41 +9,21 @@ using physiological information. `Bugphyzz` can allow a user to look at specific physiologies, and create signature sets with specific bugs. The uniform structure of the data is what allows for the latter to manifest. -We curated attributes like Gram stain, optimal temperature, fermentation, -respiration, size, shape, colony arrangement, and 27 more physiologies. -`bugphyzz` is now accessible via direct download or through our -[R package](https://github.com/waldronlab/bugphyzz/edit/main/README.md#installation). - -Here, you can find installation instructions, examples of creating signatures, -`bugphyzz`[analyses](https://github.com/waldronlab/bugphyzz/edit/main/README.md#bugphyzzanalyses) and how to add your own curation to the database. - ## Installation -You can install the development version of bugphyzz with: - ```r if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") +##Release version +BiocManager::install("bugphyzz") + ## Devel version BiocManager::install("waldronlab/bugphyzz") ``` -## Analysis using bugphyzz - -Example analyses using data from this package can be found at https://waldronlab.io/bugphyzzAnalyses/ - -## How to add a new attribute in GitHub to the bugphyzz database -Curation steps: - 1. Add attributes of physiology to [Attributes](https://github.com/waldronlab/bugphyzz/blob/main/inst/extdata/attributes.tsv) using ontology terms - 2. Add reference(s) to [Confidence in Curation](https://github.com/waldronlab/bugphyzz/blob/main/inst/extdata/confidence_in_curation.tsv) +After installation, check vignettes with: -If using Google Sheets, publish a csv file to web: - - 4. Add Google Doc "publish to web" link and add in [Link](https://github.com/waldronlab/bugphyzz/blob/main/inst/extdata/links.tsv) - 5. Add Google Doc link to [Source Link](https://github.com/waldronlab/bugphyzz/blob/main/inst/extdata/source_links.tsv) - - -## Bugphyzz worklfow - -![Bugphyzz workflow](vignettes/Drawing.svg) +```r +browseVigenttes("bugphyzz") +``` diff --git a/vignettes/Drawing.svg b/vignettes/Drawing.svg deleted file mode 100644 index a5f4e70f..00000000 --- a/vignettes/Drawing.svg +++ /dev/null @@ -1,802 +0,0 @@ - - - - - - - - - - - - - - - - - - - - G spreadsheets - - - - - BacDive - - - - Merge data and import it into Rbugphyzz:::physiologies - - - - data.frames - - - - Resolve conflicts, agreements, and double annotations - - - - Map to the NCBI tree data structure - - - - Propagate (ASR and INH) - - - - Convert to data.frame - - - - - Export text files devel and Zenodo - - - - - CSV dump files - - - - GMT files - - - - - R and outside R applications - - - - - Import into Rbugphyzz::importBugphyzz - - - - - data.frame - - - - - get signaturesbugphyzz::getBugphyzzSignatures - - - - - Optional filtering - - - - - BSEA - - - - - Data download, wrangling, and harmonization - - - waldronlab/bugphyzz - waldronlab/bugpyzzWranglingjwokaty/BacDiveRManual curation - waldronlab/bugphyzz - waldronlab/bugphyzzAnalyses - waldronlab/bugphyzzExports - sdgamboa/taxPPro - - - - - - - - - - - - - - - - - - - - - - - - - - - - Checkpoints - - diff --git a/vignettes/workflow.Rmd b/vignettes/workflow.Rmd deleted file mode 100644 index ce289f40..00000000 --- a/vignettes/workflow.Rmd +++ /dev/null @@ -1,26 +0,0 @@ ---- -title: "Bugphyzz workflow" -output: rmarkdown::html_vignette -vignette: > - %\VignetteIndexEntry{workflow} - %\VignetteEngine{knitr::rmarkdown} - %\VignetteEncoding{UTF-8} ---- - -```{r, include = FALSE} -knitr::opts_chunk$set( - collapse = TRUE, - comment = "#>" -) -``` - - -![Bugphyzz workflow](Drawing.svg) - - -## Session information - -```{r, echo=FALSE} -sessioninfo::session_info() -``` -