Dependency analysis on package ggbio

General information

Bioconductor link link
Package version1.44.0
Number of strong dependencies153
Number of all dependencies185
Number of parent packages33
Max heaviness from parent packages5
Total heaviness from parent packages12
Number of parent packages (including Suggests and Enhances)43
Max co-heaviness from parent packages ("biovizBase" and "Hmisc")22

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils stats methods graphics grDevices tools stats4 grid parallel splines BiocGenerics crayon S4Vectors IRanges RCurl GenomeInfoDbData bitops zlibbioc glue GenomeInfoDb XVector Matrix lattice rlang R6 magrittr GenomicRanges Biobase digest lifecycle pkgconfig vctrs cli Biostrings yaml tibble withr ellipsis fansi pillar utf8 MatrixGenerics DelayedArray matrixStats BiocParallel Rhtslib futile.logger snow codetools BH lambda.r futile.options formatR stringr stringi SummarizedExperiment Rsamtools jsonlite Rcpp GenomicAlignments BiocIO XML restfulr rjson fastmap png rtracklayer DBI RSQLite KEGGREST curl bit64 blob memoise plogr httr bit cachem mime openssl askpass sys progress hms prettyunits dplyr purrr tidyselect generics rappdirs AnnotationDbi biomaRt BiocFileCache xml2 dbplyr filelock assertthat GenomicFeatures gtable farver labeling munsell RColorBrewer viridisLite colorspace isoband MASS mgcv scales nlme evaluate xfun lazyeval ggplot2 highr BiocManager htmltools base64enc knitr rstudioapi BSgenome AnnotationFilter ProtGenerics plyr survival Formula latticeExtra cluster rpart nnet foreign gridExtra data.table htmlTable viridis jpeg checkmate htmlwidgets backports graph RBGL ensembldb forcats reshape tidyr cpp11 Hmisc dichromat VariantAnnotation bookdown rmarkdown jquerylib tinytex bslib sass fs brio callr desc pkgload praise processx ps waldo rprojroot diffobj rematch2 affy limma affyio preprocessCore OrganismDbi GO.db org.Hs.eg.db TxDb.Hsapiens.UCSC.hg19.knownGene 0 10 20 30 Imported methods 0 50 100 Required packages 0 5 10 Heaviness from parents methods BiocGenerics ggplot2 grid grDevices graphics stats utils gtable rlang gridExtra Biobase S4Vectors IRanges reshape2 GenomeInfoDb scales GenomicRanges Biostrings AnnotationFilter SummarizedExperiment Rsamtools GenomicAlignments rtracklayer AnnotationDbi BSgenome GGally Hmisc GenomicFeatures VariantAnnotation OrganismDbi ensembldb biovizBase tinytex knitr BiocStyle testthat vsn BSgenome.Hsapiens.UCSC.hg19 TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Mmusculus.UCSC.mm9.knownGene EnsDb.Hsapiens.v75 Homo.sapiens In total 153 packages are required directly or indirectly (185) when installing 'ggbio' (1.44.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'ggbio' Imported functions Imported S4 methods Imported S4 classes The whole namespace is imported The whole namespace is imported except some functions


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on ggbio
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ggbio. 0 0
BiocGenerics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ggbio. 4 0
ggplot2 Depends The whole set of functions/methods/classes from parent package excluding 1 objects is imported to the namespace of ggbio. 37 0
GGally Imports 1 0 0 51 5
OrganismDbi Imports 0 0 1 100 4
biovizBase Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ggbio. 141 2
reshape2 Imports 1 0 0 10 1
grid Imports 12 0 0 0 0
grDevices Imports 2 0 0 0 0
graphics Imports 1 0 0 0 0
stats Imports 3 0 0 0 0
utils Imports 2 0 0 0 0
gtable Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ggbio. 1 0
rlang Imports 4 0 0 1 0
gridExtra Imports 2 0 0 5 0
Biobase Imports 0 4 3 5 0
S4Vectors Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ggbio. 6 0
IRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ggbio. 7 0
GenomeInfoDb Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ggbio. 11 0
scales Imports 7 0 0 15 0
GenomicRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ggbio. 15 0
Biostrings Imports 0 1 0 17 0
AnnotationFilter Imports 1 0 30 17 0
SummarizedExperiment Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ggbio. 24 0
Rsamtools Imports 1 2 2 29 0
GenomicAlignments Imports 0 1 1 38 0
rtracklayer Imports 0 1 2 44 0
AnnotationDbi Imports 1 0 0 44 0
BSgenome Imports 0 0 1 45 0
Hmisc Imports 1 0 0 67 0
GenomicFeatures Imports 0 1 1 96 0
VariantAnnotation Imports 1 6 1 98 0
ensembldb Imports 0 3 1 100 0
testthat Suggests No object is imported into the namespace of ggbio. 36 12
BiocStyle Suggests No object is imported into the namespace of ggbio. 30 8
vsn Suggests No object is imported into the namespace of ggbio. 46 5
Homo.sapiens Suggests No object is imported into the namespace of ggbio. 104 4
tinytex Suggests No object is imported into the namespace of ggbio. 3 1
BSgenome.Hsapiens.UCSC.hg19 Suggests No object is imported into the namespace of ggbio. 46 1
TxDb.Hsapiens.UCSC.hg19.knownGene Suggests No object is imported into the namespace of ggbio. 97 1
TxDb.Mmusculus.UCSC.mm9.knownGene Suggests No object is imported into the namespace of ggbio. 97 1
EnsDb.Hsapiens.v75 Suggests No object is imported into the namespace of ggbio. 101 1
knitr Suggests No object is imported into the namespace of ggbio. 12 0

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 ggbio Co-heaviness as Jaccard coeffcient
Hmisc biovizBase 22 0.917

Analysis was done with pkgndep.