Dependency analysis on package openCyto

General information

Bioconductor link link
Package version2.8.0
Number of strong dependencies120
Number of all dependencies156
Number of parent packages22
Max heaviness from parent packages12
Total heaviness from parent packages20
Number of parent packages (including Suggests and Enhances)32
Max co-heaviness from parent packages ("flowStats" and "flowWorkspace")46

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports LinkingTo Suggests utils methods stats graphics grDevices stats4 tools grid splines tcltk parallel BiocGenerics Rcpp BH Biobase matrixStats cytolib S4Vectors RcppArmadillo RProtoBufLib RcppParallel Rhdf5lib lattice flowCore glue magrittr graph digest rlang R6 jsonlite zlibbioc mgcv Matrix nlme latticeExtra MASS RColorBrewer png jpeg tibble withr lifecycle vctrs pillar base64enc ellipsis fansi pkgconfig cli crayon utf8 mime mvtnorm KernSmooth hexbin XML ggplot2 RBGL Rgraphviz data.table dplyr scales aws.s3 aws.signature ncdfFlow DelayedArray gtable isoband generics tidyselect farver labeling munsell viridisLite curl httr xml2 MatrixGenerics IRanges purrr colorspace openssl askpass sys cluster robustbase pcaPP DEoptimR FNN kernlab mclust multicool plot3D pracma misc3d IDPmisc flowWorkspace R.oo R.methodsS3 flowViz fda ks rrcov corpcor mnormt fds deSolve rainbow RCurl hdrcde bitops locfit ash xfun evaluate yaml highr stringr stringi plyr gridExtra bslib htmltools jquerylib knitr tinytex sass fastmap fs rappdirs brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 openCyto ggcyto RUnit gtools flowStats flowClust clue R.utils 0 5 10 15 Imported methods 0 50 100 Required packages 0 5 10 15 Heaviness from parents methods RColorBrewer data.table gtools plyr BiocGenerics Biobase MASS lattice R.utils clue graph RBGL rrcov flowCore ncdfFlow flowClust ks flowViz flowWorkspace flowStats Rcpp flowWorkspaceData utils tools parallel markdown knitr rmarkdown testthat ggcyto CytoML In total 120 packages are required directly or indirectly (156) when installing 'openCyto' (2.8.0) Imports LinkingTo Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'openCyto' Imported functions Imported S4 classes The whole namespace is imported Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on openCyto
flowStats Imports 3 0 0 111 12
R.utils Imports 1 0 0 5 3
flowClust Imports 6 0 0 20 2
gtools Imports 1 0 0 3 1
plyr Imports 3 0 0 3 1
clue Imports 1 0 0 6 1
methods Imports 2 0 10 0 0
RColorBrewer Imports 1 0 0 0 0
data.table Imports The whole set of functions/methods/classes from parent package is imported to the namespace of openCyto. 1 0
BiocGenerics Imports 1 0 0 4 0
Biobase Imports 0 0 1 5 0
MASS Imports 1 0 0 5 0
lattice Imports Parent package is listed in Imports of openCyto but no object from parent package is imported. 5 0
graph Imports 14 0 3 6 0
RBGL Imports 1 0 0 8 0
rrcov Imports 0 0 2 12 0
flowCore Imports 7 0 4 17 0
ncdfFlow Imports 0 0 2 19 0
ks Imports 1 0 0 22 0
flowViz Imports Parent package is listed in Imports of openCyto but no object from parent package is imported. 28 0
flowWorkspace Imports 5 0 0 80 0
Rcpp LinkingTo Parent package is listed in LinkingTo of openCyto but no object from parent package is imported. 2 0
rmarkdown Suggests No object is imported into the namespace of openCyto. 27 16
testthat Suggests No object is imported into the namespace of openCyto. 36 14
knitr Suggests No object is imported into the namespace of openCyto. 12 7
CytoML Suggests No object is imported into the namespace of openCyto. 125 6
markdown Suggests No object is imported into the namespace of openCyto. 5 2
ggcyto Suggests No object is imported into the namespace of openCyto. 84 2
flowWorkspaceData Suggests No object is imported into the namespace of openCyto. 0 1
utils Suggests No object is imported into the namespace of openCyto. 0 0
tools Suggests No object is imported into the namespace of openCyto. 0 0
parallel Suggests No object is imported into the namespace of openCyto. 0 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 openCyto Co-heaviness as Jaccard coeffcient
flowWorkspace flowStats 46 0.793

Analysis was done with pkgndep.