Dependency analysis on package interactiveDisplay

General information

Bioconductor link link
Package version1.34.0
Number of strong dependencies106
Number of all dependencies198
Number of parent packages13
Max heaviness from parent packages16
Total heaviness from parent packages34
Number of parent packages (including Suggests and Enhances)28
Max co-heaviness from parent packages ("Category" and "AnnotationDbi")26

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests Enhances methods utils stats graphics grDevices tools grid stats4 splines parallel BiocGenerics Rcpp glue bitops crayon jsonlite R6 rlang Biobase IRanges S4Vectors XVector GenomeInfoDb zlibbioc RCurl GenomeInfoDbData mime fastmap cachem Matrix lattice pkgconfig vctrs cli Biostrings magrittr DBI RSQLite KEGGREST httr bit64 blob memoise plogr png curl openssl bit askpass sys XML AnnotationDbi withr ellipsis lifecycle digest yaml BH survival stringr stringi xtable htmltools base64enc rappdirs MASS mgcv nlme RColorBrewer gtable isoband scales tibble farver labeling munsell viridisLite fansi pillar colorspace utf8 htmlwidgets lazyeval graph RBGL plyr httpuv fontawesome sourcetools later promises commonmark bslib jquerylib sass fs GSEABase genefilter annotate shiny DT crosstalk matrixStats MatrixGenerics GenomicRanges DelayedArray codetools evaluate highr xfun cluster SummarizedExperiment Rsamtools GenomicAlignments BiocParallel Rhtslib BiocIO restfulr futile.logger snow rjson lambda.r futile.options formatR gtools caTools KernSmooth ggplot2 gridExtra Hmisc biovizBase BSgenome VariantAnnotation rtracklayer GenomicFeatures ensembldb AnnotationFilter Formula latticeExtra rpart nnet foreign data.table htmlTable viridis dichromat biomaRt dplyr progress ProtGenerics jpeg knitr checkmate rstudioapi BiocFileCache xml2 generics tidyselect hms prettyunits purrr backports dbplyr filelock assertthat permute limma glmnet foreach gplots Wrench shape RcppEigen iterators locfit org.Hs.eg.db Category GO.db AnnotationForge Rgraphviz reshape2 OrganismDbi GGally BiocManager forcats reshape tidyr cpp11 0 5 10 15 Imported methods 0 50 100 150 Required packages 0 20 40 60 Heaviness from parents methods grid BiocGenerics RColorBrewer XML plyr gridSVG reshape2 shiny ggplot2 interactiveDisplayBase AnnotationDbi Category RUnit Biobase gplots knitr vegan GenomicRanges SummarizedExperiment metagenomeSeq rtracklayer GO.db hgu95av2.db GOstats Gviz ggbio rstudio In total 106 packages are required directly or indirectly (198) when installing 'interactiveDisplay' (1.34.0) Depends Imports Suggests Enhances Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'interactiveDisplay' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on interactiveDisplay
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of interactiveDisplay. 0 0
grid Depends 1 0 0 0 0
BiocGenerics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of interactiveDisplay. 4 0
ggplot2 Imports 15 0 0 37 16
Category Imports The whole set of functions/methods/classes from parent package is imported to the namespace of interactiveDisplay. 58 8
interactiveDisplayBase Imports The whole set of functions/methods/classes from parent package is imported to the namespace of interactiveDisplay. 41 6
reshape2 Imports 1 0 0 10 3
gridSVG Imports 1 0 0 7 1
RColorBrewer Imports 1 0 0 0 0
XML Imports 1 0 0 2 0
plyr Imports 1 0 0 3 0
shiny Imports The whole set of functions/methods/classes from parent package is imported to the namespace of interactiveDisplay. 34 0
AnnotationDbi Imports The whole set of functions/methods/classes from parent package is imported to the namespace of interactiveDisplay. 44 0
ggbio Suggests No object is imported into the namespace of interactiveDisplay. 153 68
Gviz Suggests No object is imported into the namespace of interactiveDisplay. 142 61
rtracklayer Suggests No object is imported into the namespace of interactiveDisplay. 44 20
metagenomeSeq Suggests No object is imported into the namespace of interactiveDisplay. 30 16
SummarizedExperiment Suggests No object is imported into the namespace of interactiveDisplay. 24 5
gplots Suggests No object is imported into the namespace of interactiveDisplay. 7 4
knitr Suggests No object is imported into the namespace of interactiveDisplay. 12 4
GOstats Suggests No object is imported into the namespace of interactiveDisplay. 62 4
vegan Suggests No object is imported into the namespace of interactiveDisplay. 14 3
hgu95av2.db Suggests No object is imported into the namespace of interactiveDisplay. 46 2
RUnit Suggests No object is imported into the namespace of interactiveDisplay. 3 1
GenomicRanges Suggests No object is imported into the namespace of interactiveDisplay. 15 1
GO.db Suggests No object is imported into the namespace of interactiveDisplay. 45 1
Biobase Suggests No object is imported into the namespace of interactiveDisplay. 5 0
rstudio Enhances No object is imported into the namespace of interactiveDisplay. 0 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 interactiveDisplay Co-heaviness as Jaccard coeffcient
AnnotationDbi Category 26 0.765
shiny interactiveDisplayBase 14 0.700

Analysis was done with pkgndep.