Dependency analysis on package ReactomePA

General information

Bioconductor link link
Package version1.40.0
Number of strong dependencies128
Number of all dependencies161
Number of parent packages8
Max heaviness from parent packages14
Total heaviness from parent packages18
Number of parent packages (including Suggests and Enhances)15
Max co-heaviness from parent packages ("enrichplot" and "DOSE")21

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of ReactomePA and columns are the dependency packages that each parent package brings in. On the right side of the heatmap, there are three barplot annotations: 1. number of imported functions/S4 methods/S4 classes from parent packages; 2. number of dependency packages from each parent package; 3. heaviness of each parent package on ReactomePA.

Adjust heatmap size:
Base packages Other packages Imports Suggests methods utils stats grDevices tools graphics stats4 grid splines parallel glue rlang R6 pkgconfig magrittr jsonlite vctrs crayon cli fastmap digest Rcpp BiocGenerics Biobase IRanges DBI RSQLite S4Vectors KEGGREST bit64 blob memoise plogr httr png Biostrings bit cachem curl mime openssl XVector GenomeInfoDb askpass zlibbioc RCurl GenomeInfoDbData sys bitops stringr stringi Matrix lattice tibble withr lifecycle ellipsis fansi pillar utf8 AnnotationDbi gtable isoband MASS mgcv scales nlme farver labeling munsell RColorBrewer viridisLite colorspace rappdirs ggplot2 gridExtra igraph purrr dplyr ggforce ggrepel viridis tidygraph graphlayouts tidyr generics tidyselect tweenr polyclip RcppEigen cpp11 RcppArmadillo BiocParallel DO.db fgsea GOSemSim qvalue reshape2 futile.logger snow codetools BH data.table fastmatch GO.db plyr lambda.r futile.options formatR aplot DOSE ggraph scatterpie shadowtext ggtree yulab.utils ggfun ggplotify patchwork ape tidytree treeio gridGraphics lazyeval graph evaluate yaml xfun highr knitr htmltools jquerylib tinytex bslib base64enc sass fs rmarkdown bookdown BiocManager brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 downloader enrichplot 0 2 4 6 8 Imported methods 0 50 100 Required packages 0 5 10 15 Heaviness from parents igraph ggplot2 AnnotationDbi reactome.db graphite ggraph DOSE enrichplot knitr rmarkdown prettydoc BiocStyle testthat org.Hs.eg.db clusterProfiler In total 128 packages are required directly or indirectly (161) when installing 'ReactomePA' (1.40.0) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'ReactomePA' Imported functions Imported S4 methods Imported S4 classes


Dependency table

"Import" information is from the NAMESPACE file of ReactomePA.

imports: number of imported functions/objects; importMethods: number of imported S4 methods; importClasses: number of imported S4 classes.

Required packages: number of strong dependency packages for each of the parent package (or in other words, number of dependency packages the parent package brings in).

Heaviness from parent on ReactomePA: number of required packages that can be reduced if moving parent package to Suggests of ReactomePA.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on ReactomePA
enrichplot Imports 6 0 0 123 14
graphite Imports 2 0 0 47 3
reactome.db Imports 3 0 0 45 1
igraph Imports 6 0 0 10 0
ggplot2 Imports 4 0 0 37 0
AnnotationDbi Imports 0 2 0 44 0
ggraph Imports 4 0 0 57 0
DOSE Imports 4 2 2 92 0
BiocStyle Suggests No object is imported into the namespace of ReactomePA. 30 16
prettydoc Suggests No object is imported into the namespace of ReactomePA. 28 14
testthat Suggests No object is imported into the namespace of ReactomePA. 36 14
rmarkdown Suggests No object is imported into the namespace of ReactomePA. 27 13
knitr Suggests No object is imported into the namespace of ReactomePA. 12 5
clusterProfiler Suggests No object is imported into the namespace of ReactomePA. 125 2
org.Hs.eg.db Suggests No object is imported into the namespace of ReactomePA. 45 1

The following table lists pairs of parent packages with co-heaviness larger than 10. The co-heaviness measures the number of additional dependencies that two parent packages simultaneously import and are only imported by the two parents.

Note the co-heaviness from parents can be always easily observed in the dependency heatmap.

Parent 1 Parent 2 Co-heaviness on ReactomePA Co-heaviness as Jaccard coeffcient
DOSE enrichplot 21 0.600
ggraph enrichplot 16 0.533

Analysis was done with pkgndep.