Dependency analysis on package InteractiveComplexHeatmap

General information

Bioconductor link link
Package version1.4.0
Number of strong dependencies96
Number of all dependencies280
Number of parent packages17
Max heaviness from parent packages35
Total heaviness from parent packages58
Number of parent packages (including Suggests and Enhances)48
Max co-heaviness from parent packages ("kableExtra" and "shiny")12

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils methods stats grDevices graphics tools grid stats4 parallel splines tcltk datasets digest BiocGenerics rlang crayon S4Vectors glue IRanges R6 Rcpp magrittr colorspace fastmap jsonlite RColorBrewer png matrixStats mime lifecycle pkgconfig vctrs cli ellipsis codetools withr GlobalOptions base64enc cachem httr tibble curl openssl fansi pillar askpass utf8 sys shape rjson htmltools rappdirs stringr scales viridisLite stringi farver labeling munsell circlize foreach doParallel cluster iterators jquerylib xml2 yaml GetoptLong clue bslib sass fs evaluate xfun highr cpp11 xtable later promises knitr httpuv fontawesome sourcetools commonmark rstudioapi tinytex callr processx ps systemfonts rvest rmarkdown selectr webshot svglite bitops RCurl lattice GenomeInfoDb XVector GenomeInfoDbData zlibbioc Matrix Biobase GenomicRanges gtable mgcv nlme MatrixGenerics DelayedArray DBI bit64 blob bit SummarizedExperiment AnnotationDbi RSQLite Biostrings KEGGREST memoise plogr ggplot2 isoband MASS ComplexHeatmap KernSmooth RcppArmadillo dplyr purrr tidyselect generics BH gtools caTools BiocParallel futile.logger snow lambda.r futile.options formatR XML progress hms prettyunits dbplyr assertthat markdown mvtnorm mclust polylabelr brew shiny rematch2 locfit slam irlba tidyr viridis gridExtra SingleCellExperiment biomaRt BiocFileCache filelock gplots htmlwidgets crosstalk lazyeval jpeg FNN kernlab multicool plot3D pracma misc3d HilbertVis hash BiocManager BiocVersion brio desc pkgload praise waldo rprojroot diffobj skmeans microbenchmark impute eulerr GenSA polyclip dendextend patchwork GOSemSim tm GO.db org.Hs.eg.db proxyC NLP RcppParallel scuttle DelayedMatrixStats beachmat BiocNeighbors BiocSingular ggbeeswarm Rtsne RcppML ggrepel sparseMatrixStats RcppHNSW ScaledMatrix rsvd beeswarm vipor RcppEigen randomForest genefilter geneplotter annotate survival BiocIO rtracklayer Rsamtools GenomicAlignments restfulr Rhtslib e1071 doRNG pheatmap ROCR robustbase rrcov WriteXLS class proxy rngtools DEoptimR pcaPP broom dtplyr forcats googledrive googlesheets4 haven lubridate modelr readr readxl reprex backports data.table gargle uuid cellranger ids clipr vroom tzdb rematch 0 2 4 6 8 Imported methods 0 50 100 Required packages 0 20 40 Heaviness from parents ComplexHeatmap grDevices stats grid utils clisymbols RColorBrewer digest jsonlite svglite GetoptLong S4Vectors htmltools IRanges fontawesome shiny kableExtra data.table BiocManager cluster gplots circlize knitr GenomicRanges pheatmap DT gridtext ks SummarizedExperiment SingleCellExperiment airway rmarkdown HilbertCurve pkgndep shinydashboard testthat EnrichedHeatmap org.Hs.eg.db GO.db cola tidyHeatmap simplifyEnrichment scater GOexpress DESeq2 GenomicFeatures SC3 tidyverse In total 96 packages are required directly or indirectly (280) when installing 'InteractiveComplexHeatmap' (1.4.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'InteractiveComplexHeatmap' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on InteractiveComplexHeatmap
ComplexHeatmap Depends The whole set of functions/methods/classes from parent package is imported to the namespace of InteractiveComplexHeatmap. 28 12
kableExtra Imports 5 0 0 63 35
shiny Imports The whole set of functions/methods/classes from parent package is imported to the namespace of InteractiveComplexHeatmap. 34 10
clisymbols Imports The whole set of functions/methods/classes from parent package is imported to the namespace of InteractiveComplexHeatmap. 0 1
grDevices Imports 8 0 0 0 0
stats Imports 4 0 0 0 0
grid Imports The whole set of functions/methods/classes from parent package is imported to the namespace of InteractiveComplexHeatmap. 0 0
utils Imports 5 0 0 0 0
RColorBrewer Imports The whole set of functions/methods/classes from parent package is imported to the namespace of InteractiveComplexHeatmap. 0 0
digest Imports The whole set of functions/methods/classes from parent package is imported to the namespace of InteractiveComplexHeatmap. 1 0
jsonlite Imports 2 0 0 1 0
svglite Imports The whole set of functions/methods/classes from parent package is imported to the namespace of InteractiveComplexHeatmap. 2 0
GetoptLong Imports The whole set of functions/methods/classes from parent package is imported to the namespace of InteractiveComplexHeatmap. 6 0
S4Vectors Imports The whole set of functions/methods/classes from parent package is imported to the namespace of InteractiveComplexHeatmap. 6 0
htmltools Imports 1 0 0 6 0
IRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of InteractiveComplexHeatmap. 7 0
fontawesome Imports The whole set of functions/methods/classes from parent package is imported to the namespace of InteractiveComplexHeatmap. 7 0
GenomicFeatures Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 96 50
scater Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 85 48
tidyverse Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 107 46
GOexpress Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 93 45
DESeq2 Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 93 45
SC3 Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 100 40
simplifyEnrichment Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 76 30
tidyHeatmap Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 68 20
org.Hs.eg.db Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 45 18
GO.db Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 45 18
ks Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 22 16
cola Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 64 16
SingleCellExperiment Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 25 14
airway Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 25 14
SummarizedExperiment Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 24 13
HilbertCurve Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 27 11
EnrichedHeatmap Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 40 10
testthat Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 36 9
GenomicRanges Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 15 7
gplots Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 7 5
gridtext Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 20 5
pkgndep Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 33 5
DT Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 20 4
pheatmap Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 18 2
data.table Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 1 1
BiocManager Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 1 1
shinydashboard Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 35 1
cluster Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 4 0
circlize Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 9 0
knitr Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 12 0
rmarkdown Suggests No object is imported into the namespace of InteractiveComplexHeatmap. 27 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 InteractiveComplexHeatmap Co-heaviness as Jaccard coeffcient
shiny kableExtra 12 0.211

Analysis was done with pkgndep.