--- title: "Overview of BiocPkgTools" author: - name: Shian Su affiliation: Walter and Eliza Hall Institute, Melbourne, Australia - name: Vince Carey affiliation: Channing Lab, Brigham and Womens Hospital, Harvard University, Boston, MA USA - name: Marcel Ramos affiliation: Roswell Park Comprehensive Cancer Center, Buffalo, NY USA - name: Lori Shepherd affiliation: Roswell Park Comprehensive Cancer Center, Buffalo, NY USA - name: Martin Morgan affiliation: Roswell Park Comprehensive Cancer Center, Buffalo, NY USA - name: Sean Davis affiliation: National Cancer Institute, National Institutes of Health, Bethesda, MD USA email: seandavi@gmail.com package: BiocPkgTools output: BiocStyle::html_document: toc: false abstract: | Bioconductor has a rich ecosystem of metadata around packages, usage, and build status. This package is a simple collection of functions to access that metadata from R in a tidy data format. The goal is to expose metadata for data mining and value-added functionality such as package searching, text mining, and analytics on packages. vignette: | %\VignetteIndexEntry{Overview of BiocPkgTools} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- # Introduction Bioconductor has a rich ecosystem of metadata around packages, usage, and build status. This package is a simple collection of functions to access that metadata from R in a tidy data format. The goal is to expose metadata for data mining and value-added functionality such as package searching, text mining, and analytics on packages. Functionality includes access to : - Download statistics - General package listing - Build reports - Package dependency graphs - Vignettes ```{r init, include=FALSE} library(knitr) opts_chunk$set(warning = FALSE, message = FALSE, cache=FALSE) ``` ```{r style, echo = FALSE, results = 'asis'} BiocStyle::markdown() ``` # Build reports The Bioconductor build reports are available online as HTML pages. However, they are not very computable. The `biocBuildReport` function does some heroic parsing of the HTML to produce a *tidy* data.frame for further processing in R. ```{r} library(BiocPkgTools) head(biocBuildReport()) ``` ## Personal build report Because developers may be interested in a quick view of their own packages, there is a simple function, `problemPage`, to produce an HTML report of the build status of packages matching a given author *regex* supplied to the `authorPattern` argument. The default is to report only "problem" build statuses (ERROR, WARNING). ```{r eval=FALSE} problemPage(authorPattern = "V.*Carey") ``` In similar fashion, maintainers of packages that have many downstream packages that depend on them may wish to check that a change they introduced hasn't suddenly broken a large number of these. You can use the `dependsOn` argument to produce the summary report of those packages that "depend on" the given package. ```{r eval=FALSE} problemPage(dependsOn = "limma") ``` When run in an interactive environment, the `problemPage` function will open a browser window for user interaction. Note that if you want to include all your package results, not just the broken ones, simply specify `includeOK = TRUE`. # Download statistics Bioconductor supplies download stats for all packages. The `biocDownloadStats` function grabs all available download stats for all packages in all Experiment Data, Annotation Data, and Software packages. The results are returned as a tidy data.frame for further analysis. ```{r} head(biocDownloadStats()) ``` The download statistics reported are for ***all available versions*** of a package. There are no separate, publicly available statistics broken down by version. The majority of Bioconductor Software packages are also available through other channels such as Anaconda, who also provided download statistics for packages installed from their repositories. Access to these counts is provided by the `anacondaDownloadStats` function: ```{r} head(anacondaDownloadStats()) ``` Note that Anaconda do not provide counts for distinct IP addresses, but this column is included for compatibility with the Bioconductor count tables. # Package details The R `DESCRIPTION` file contains a plethora of information regarding package authors, dependencies, versions, etc. In a repository such as Bioconductor, these details are available in bulk for all included packages. The `biocPkgList` returns a data.frame with a row for each package. Tons of information are available, as evidenced by the column names of the results. ```{r} bpi = biocPkgList() colnames(bpi) ``` Some of the variables are parsed to produce `list` columns. ```{r} head(bpi) ``` As a simple example of how these columns can be used, extracting the `importsMe` column to find the packages that import the `r Biocpkg("GEOquery")` package. ```{r} require(dplyr) bpi = biocPkgList() bpi %>% filter(Package=="GEOquery") %>% pull(importsMe) %>% unlist() ``` # Package Explorer For the end user of Bioconductor, an analysis often starts with finding a package or set of packages that perform required tasks or are tailored to a specific operation or data type. The `biocExplore()` function implements an interactive bubble visualization with filtering based on biocViews terms. Bubbles are sized based on download statistics. Tooltip and detail-on-click capabilities are included. To start a local session: ```{r biocExplore} biocExplore() ``` # Dependency graphs The Bioconductor ecosystem is built around the concept of interoperability and dependencies. These interdependencies are available as part of the `biocPkgList()` output. The `BiocPkgTools` provides some convenience functions to convert package dependencies to R graphs. A modular approach leads to the following workflow. 1. Create a `data.frame` of dependencies using `buildPkgDependencyDataFrame`. 2. Create an `igraph` object from the dependency data frame using `buildPkgDependencyIgraph` 3. Use native `igraph` functionality to perform arbitrary network operations. Convenience functions, `inducedSubgraphByPkgs` and `subgraphByDegree` are available. 4. Visualize with packages such as `r CRANpkg("visNetwork")`. ## Working with dependency graphs A dependency graph for all of Bioconductor is a starting place. ```{r} dep_df = buildPkgDependencyDataFrame() g = buildPkgDependencyIgraph(dep_df) g library(igraph) head(V(g)) head(E(g)) ``` See `inducedSubgraphByPkgs` and `subgraphByDegree` to produce subgraphs based on a subset of packages. See the igraph documentation for more detail on graph analytics, setting vertex and edge attributes, and advanced subsetting. ## Graph visualization The visNetwork package is a nice interactive visualization tool that implements graph plotting in a browser. It can be integrated into shiny applications. Interactive graphs can also be included in Rmarkdown documents (see vignette) ```{r} igraph_network = buildPkgDependencyIgraph(buildPkgDependencyDataFrame()) ``` The full dependency graph is really not that informative to look at, though doing so is possible. A common use case is to visualize the graph of dependencies "centered" on a package of interest. In this case, I will focus on the `r Biocpkg("GEOquery")` package. ```{r} igraph_geoquery_network = subgraphByDegree(igraph_network, "GEOquery") ``` The `subgraphByDegree()` function returns all nodes and connections within `degree` of the named package; the default `degree` is `1`. The visNework package can plot `igraph` objects directly, but more flexibility is offered by first converting the graph to visNetwork form. ```{r} library(visNetwork) data <- toVisNetworkData(igraph_geoquery_network) ``` The next few code chunks highlight just a few examples of the visNetwork capabilities, starting with a basic plot. ```{r } visNetwork(nodes = data$nodes, edges = data$edges, height = "500px") ``` For fun, we can watch the graph stabilize during drawing, best viewed interactively. ```{r} visNetwork(nodes = data$nodes, edges = data$edges, height = "500px") %>% visPhysics(stabilization=FALSE) ``` Add arrows and colors to better capture dependencies. ```{r} data$edges$color='lightblue' data$edges[data$edges$edgetype=='Imports','color']= 'red' data$edges[data$edges$edgetype=='Depends','color']= 'green' visNetwork(nodes = data$nodes, edges = data$edges, height = "500px") %>% visEdges(arrows='from') ``` Add a legend. ```{r} ledges <- data.frame(color = c("green", "lightblue", "red"), label = c("Depends", "Suggests", "Imports"), arrows =c("from", "from", "from")) visNetwork(nodes = data$nodes, edges = data$edges, height = "500px") %>% visEdges(arrows='from') %>% visLegend(addEdges=ledges) ``` ## Integration with `r Biocpkg("BiocViews")` [Work in progress] The `r Biocpkg("biocViews")` package is a small ontology of terms describing Bioconductor packages. This is a work-in-progress section, but here is a small example of plotting the biocViews graph. ```{r biocViews} library(biocViews) data(biocViewsVocab) biocViewsVocab library(igraph) g = igraph.from.graphNEL(biocViewsVocab) library(visNetwork) gv = toVisNetworkData(g) visNetwork(gv$nodes, gv$edges, width="100%") %>% visIgraphLayout(layout = "layout_as_tree", circular=TRUE) %>% visNodes(size=20) %>% visPhysics(stabilization=FALSE) ``` # Dependency burden The dependency burden of a package, namely the amount of functionality that a given package is importing, is an important parameter to take into account during package development. A package may break because one or more of its dependencies have changed the part of the API our package is importing or this part has even broken. For this reason, it may be useful for package developers to quantify the dependency burden of a given package. To do that we should first gather all dependency information using the function `buildPkgDependencyDataFrame()` but setting the arguments to work with packages in Bioconductor and CRAN and dependencies categorised as `Depends` or `Imports`, which are the ones installed by default for a given package. ```{r} depdf <- buildPkgDependencyDataFrame(repo=c("BioCsoft", "CRAN"), dependencies=c("Depends", "Imports")) dim(depdf) head(depdf) # too big to show all ``` Finally, we call the function `pkgDepMetrics()` to obtain different metrics on the dependency burden of a package we want to analyze, in the case below, the package `BiocPkgTools` itself: ```{r} pkgDepMetrics("BiocPkgTools", depdf) ``` In this resulting table, rows correspond to dependencies and columns provide the following information: * `ImportedAndUsed`: number of functionality calls imported and used in the package. * `Exported`: number of functionality calls exported by the dependency. * `Usage`: (`ImportedAndUsed`x 100) / `Exported`. This value provides an estimate of what fraction of the functionality of the dependency is actually used in the given package. * `DepOverlap`: Similarity between the dependency graph structure of the given package and the one of the dependency in the corresponding row, estimated as the [Jaccard index](https://en.wikipedia.org/wiki/Jaccard_index) between the two sets of vertices of the corresponding graphs. Its values goes between 0 and 1, where 0 indicates that no dependency is shared, while 1 indicates that the given package and the corresponding dependency depend on an identical subset of packages. * `DepGainIfExcluded`: The 'dependency gain' (decrease in the total number of dependencies) that would be obtained if this package was excluded from the list of direct dependencies. The reported information is ordered by the `Usage` column to facilitate the identification of dependencies for which the analyzed package is using a small fraction of their functionality and therefore, it could be easier remove them. To aid in that decision, the column `DepOverlap` reports the overlap of the dependency graph of each dependency with the one of the analyzed package. Here a value above, e.g., 0.5, could, albeit not necessarily, imply that removing that dependency could substantially lighten the dependency burden of the analyzed package. An `NA` value in the `ImportedAndUsed` column indicates that the function `pkgDepMetrics()` could not identify what functionality calls in the analyzed package are made to the dependency. This may happen because `pkgDepMetrics()` has failed to identify the corresponding calls, as it happens with imported built-in constants such as `DNA_BASES` from `Biostrings`, or that although the given package is importing that dependency, none of its functionality is actually being used. In such a case, this dependency could be safely removed without any further change in the analyzed package. We can find out what actually functionality calls are we importing as follows: ```{r} imp <- pkgDepImports("BiocPkgTools") imp %>% filter(pkg == "DT") ``` # Identities of maintainers It is important to be able to identify the maintainer of a package in a reliable way. The DESCRIPTION file for a package can include an `Authors@R` field. This field can capture metadata about maintainers and contributors in a programmatically accessible way. Each element of the role field of a `person` (see `?person`) in the `Authors@R` field comes from a subset of the [relations vocabulary of the Library of Congress](https://www.loc.gov/marc/relators/relaterm.html). Metadata about maintainers can be extracted from DESCRIPTION in various ways. As of October 2022, we focus on the use of the ORCID field which is an optional `comment` component in a `person` element. For example, in the DESCRIPTION for the AnVIL package we have ``` Authors@R: c(person( "Martin", "Morgan", role = c("aut", "cre"), email = "mtmorgan.bioc@gmail.com", comment = c(ORCID = "0000-0002-5874-8148") ), ``` This convention is used for a fair number of Bioconductor and CRAN packages. We'll demonstrate the use of `get_cre_orcids` with some packages. ```{r demoorc} inst = rownames(installed.packages()) cands = c("devtools", "evaluate", "ggplot2", "GEOquery", "gert", "utils") totry = intersect(cands, inst) oids = get_cre_orcids(totry) oids ``` We use the ORCID API to tabulate metadata about the holders of these IDs. We'll avoid evaluating this because a token must be refreshed for the query to succeed. ```{r lktab,eval=FALSE} orcid_table(oids) ``` In October 2022 the result is ``` > orcid_table(.Last.value) name org devtools Jennifer Bryan RStudio evaluate Yihui Xie RStudio, Inc. ggplot2 Thomas Lin Pedersen RStudio GEOquery Sean Davis University of Colorado Anschutz Medical Campus gert Jeroen Ooms Berkeley Institute for Data Science utils city region country orcid devtools Boston MA US 0000-0002-6983-2759 evaluate Elkhorn NE US 0000-0003-0645-5666 ggplot2 Copenhagen DK 0000-0002-5147-4711 GEOquery Aurora Colorado US 0000-0002-8991-6458 gert Berkeley CA US 0000-0002-4035-0289 utils ``` # Provenance ```{r} sessionInfo() ```