Dependency analysis on package ggcyto

General information

Bioconductor link link
Package version1.24.0
Number of strong dependencies84
Number of all dependencies155
Number of parent packages12
Max heaviness from parent packages27
Total heaviness from parent packages30
Number of parent packages (including Suggests and Enhances)21
Max co-heaviness from parent packages ("flowWorkspace" and "ggplot2")19

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils methods grDevices stats graphics grid tools stats4 splines tcltk parallel glue rlang R6 magrittr Rcpp digest lifecycle tibble withr RColorBrewer ellipsis fansi pillar pkgconfig vctrs lattice cli crayon utf8 Biobase BiocGenerics matrixStats cytolib S4Vectors RcppArmadillo BH RProtoBufLib RcppParallel Rhdf5lib gtable MASS farver labeling munsell viridisLite colorspace jsonlite flowCore isoband mgcv scales nlme Matrix base64enc zlibbioc latticeExtra ggplot2 png jpeg xml2 XML graph RBGL Rgraphviz data.table dplyr aws.s3 aws.signature ncdfFlow DelayedArray generics tidyselect curl httr MatrixGenerics IRanges purrr mime openssl askpass sys evaluate KernSmooth hexbin IDPmisc highr stringr yaml xfun stringi htmltools fastmap brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 plyr flowWorkspace flowViz fda cluster ks rrcov corpcor mnormt fds deSolve FNN kernlab mclust multicool mvtnorm plot3D pracma robustbase pcaPP rainbow RCurl misc3d DEoptimR hdrcde bitops locfit ash bslib jquerylib knitr tinytex sass fs rappdirs testthat cpp11 gtools flowStats flowClust clue R.utils R.oo R.methodsS3 0 2 4 6 Imported methods 0 50 100 Required packages 0 10 20 30 Heaviness from parents methods flowCore ncdfFlow ggplot2 flowWorkspace RColorBrewer data.table rlang plyr gridExtra hexbin scales flowWorkspaceData knitr rmarkdown flowViz testthat ggridges vdiffr flowStats openCyto In total 84 packages are required directly or indirectly (155) when installing 'ggcyto' (1.24.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'ggcyto' Imported functions 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 ggcyto.

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on ggcyto
flowWorkspace Depends 4 0 0 80 27
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ggcyto. 0 0
flowCore Depends 1 0 0 17 0
ncdfFlow Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ggcyto. 19 0
ggplot2 Depends 2 0 0 37 0
plyr Imports 6 0 0 3 1
gridExtra Imports 1 0 0 5 1
hexbin Imports 2 0 0 7 1
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 ggcyto. 1 0
rlang Imports 2 0 0 1 0
scales Imports Parent package is listed in Imports of ggcyto but no object from parent package is imported. 15 0
openCyto Suggests No object is imported into the namespace of ggcyto. 120 38
flowStats Suggests No object is imported into the namespace of ggcyto. 111 30
vdiffr Suggests No object is imported into the namespace of ggcyto. 42 18
rmarkdown Suggests No object is imported into the namespace of ggcyto. 27 16
testthat Suggests No object is imported into the namespace of ggcyto. 36 14
knitr Suggests No object is imported into the namespace of ggcyto. 12 7
flowViz Suggests No object is imported into the namespace of ggcyto. 28 3
flowWorkspaceData Suggests No object is imported into the namespace of ggcyto. 0 1
ggridges Suggests No object is imported into the namespace of ggcyto. 40 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 ggcyto Co-heaviness as Jaccard coeffcient
ggplot2 flowWorkspace 19 0.413

Analysis was done with pkgndep.