Get biocViews Co-Occurrence Counts

Usage

get_view_cooccurrences(view, pkg_list = NULL, keep_self = FALSE, ratio = FALSE)

Arguments

view: A biocViews term.
pkg_list: Value of a call to biocPkgList(). If NULL (default), will call biocPkgList() internally. See Details.
keep_self: Logical. Include view itself in the output.
ratio: Logical. Return fraction of packages annotated with view also annotated with each other term, rather than raw counts.

Value

A tibble of two columns: date and cooccurences. package is a biocViews term. value is the number (or fraction, if ratio = TRUE) of packages associated with both view and package.

Details

Calling BiocPkgTools::biocPkgList() and passing the result to get_packages_by_view() or get_packages_by_views() is more efficient if you are making multiple calls. See vignette 'Optimisations' for a more comprehensive discussion and demonstration.

Examples

library(dplyr)
#> 
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union
get_view_cooccurrences("Spatial") |>
  arrange(desc(value))
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://p3m.dev/cran/__linux__/noble/latest
#> # A tibble: 65 × 2
#>    package            value
#>    <chr>              <int>
#>  1 Transcriptomics       51
#>  2 SingleCell            49
#>  3 GeneExpression        42
#>  4 DataImport            18
#>  5 RNASeq                15
#>  6 Clustering            14
#>  7 ImmunoOncology        10
#>  8 DataRepresentation     8
#>  9 CellBasedAssays        7
#> 10 QualityControl         7
#> # ℹ 55 more rows