Dependency analysis on package WGCNA

General information

CRAN link link
Package version1.71
Number of strong dependencies108
Number of all dependencies113
Number of parent packages17
Max heaviness from parent packages47
Total heaviness from parent packages54
Number of parent packages (including Suggests and Enhances)22
Max co-heaviness from parent packages ("GO.db" and "AnnotationDbi")28

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of WGCNA 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 WGCNA.

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils stats methods grDevices graphics tools stats4 grid splines parallel glue rlang png fastmap R6 pkgconfig vctrs jsonlite cli crayon BiocGenerics Biobase IRanges DBI RSQLite S4Vectors KEGGREST bit64 blob memoise Rcpp plogr httr Biostrings bit cachem curl mime openssl XVector GenomeInfoDb askpass zlibbioc RCurl GenomeInfoDbData sys bitops AnnotationDbi codetools iterators lattice Matrix foreach survival Formula ggplot2 latticeExtra cluster rpart nnet foreign gtable gridExtra data.table htmlTable viridis htmltools base64enc digest isoband MASS mgcv scales tibble withr jpeg RColorBrewer stringr knitr magrittr checkmate htmlwidgets rstudioapi viridisLite nlme farver labeling lifecycle munsell ellipsis fansi pillar stringi evaluate highr yaml xfun backports colorspace utf8 infotheo 0 10 20 30 Imported methods 0 20 40 60 Required packages 0 20 40 Heaviness from parents fastcluster dynamicTreeCut stats grDevices utils matrixStats impute splines parallel preprocessCore Rcpp foreach doParallel survival AnnotationDbi GO.db Hmisc infotheo entropy minet org.Hs.eg.db org.Mm.eg.db In total 108 packages are required directly or indirectly (113) when installing 'WGCNA' (1.71) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'WGCNA' Imported functions The whole namespace is imported


Dependency table

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

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 WGCNA: number of required packages that can be reduced if moving parent package to Suggests of WGCNA.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on WGCNA
fastcluster Depends The whole set of functions/methods/classes from parent package is imported to the namespace of WGCNA. 0 1
dynamicTreeCut Depends The whole set of functions/methods/classes from parent package is imported to the namespace of WGCNA. 1 1
Hmisc Imports 2 0 0 67 47
matrixStats Imports The whole set of functions/methods/classes from parent package is imported to the namespace of WGCNA. 0 1
impute Imports 1 0 0 0 1
preprocessCore Imports 1 0 0 1 1
doParallel Imports The whole set of functions/methods/classes from parent package is imported to the namespace of WGCNA. 5 1
GO.db Imports The whole set of functions/methods/classes from parent package is imported to the namespace of WGCNA. 45 1
stats Imports 35 0 0 0 0
grDevices Imports 6 0 0 0 0
utils Imports 8 0 0 0 0
splines Imports 1 0 0 0 0
parallel Imports 2 0 0 0 0
Rcpp Imports 1 0 0 2 0
foreach Imports The whole set of functions/methods/classes from parent package is imported to the namespace of WGCNA. 3 0
survival Imports 3 0 0 9 0
AnnotationDbi Imports The whole set of functions/methods/classes from parent package is imported to the namespace of WGCNA. 44 0
minet Suggests No object is imported into the namespace of WGCNA. 1 2
infotheo Suggests No object is imported into the namespace of WGCNA. 0 1
entropy Suggests No object is imported into the namespace of WGCNA. 0 1
org.Hs.eg.db Suggests No object is imported into the namespace of WGCNA. 45 1
org.Mm.eg.db Suggests No object is imported into the namespace of WGCNA. 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 WGCNA Co-heaviness as Jaccard coeffcient
AnnotationDbi GO.db 28 0.966

Analysis was done with pkgndep.