Dependency analysis on package flowStats

General information

Bioconductor link link
Package version4.8.0
Number of strong dependencies111
Number of all dependencies139
Number of parent packages21
Max heaviness from parent packages25
Total heaviness from parent packages42
Number of parent packages (including Suggests and Enhances)28
Max co-heaviness from parent packages ("flowWorkspace" and "fda")25

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests Enhances stats utils graphics methods grDevices grid stats4 splines tools tcltk parallel BiocGenerics Rcpp lattice BH Biobase matrixStats cytolib S4Vectors RcppArmadillo RProtoBufLib RcppParallel Rhdf5lib mgcv Matrix nlme RColorBrewer MASS digest glue rlang tibble withr lifecycle magrittr R6 vctrs pillar ellipsis fansi pkgconfig cli crayon utf8 flowCore ggplot2 scales gtable isoband farver labeling munsell viridisLite colorspace mvtnorm zlibbioc KernSmooth latticeExtra png jpeg graph jsonlite pcaPP FNN kernlab mclust multicool plot3D pracma misc3d hexbin XML RBGL Rgraphviz data.table dplyr aws.s3 aws.signature ncdfFlow DelayedArray generics tidyselect curl httr xml2 base64enc MatrixGenerics IRanges purrr mime openssl askpass sys robustbase DEoptimR IDPmisc fds deSolve rainbow RCurl hdrcde cluster ks bitops locfit ash plyr flowWorkspace brio callr desc evaluate pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 gridExtra gtools flowViz flowStats flowClust clue rrcov R.utils fda corpcor mnormt R.oo R.methodsS3 0 10 20 30 Imported methods 0 50 100 Required packages 0 10 20 Heaviness from parents methods grDevices graphics stats utils RColorBrewer mnormt KernSmooth corpcor BiocGenerics cluster MASS Biobase lattice rrcov flowCore ncdfFlow ks flowViz fda flowWorkspace xtable testthat ggridges ggcyto openCyto graph RBGL In total 111 packages are required directly or indirectly (139) when installing 'flowStats' (4.8.0) Imports Suggests Enhances Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'flowStats' Imported functions Imported S4 methods Imported S4 classes The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on flowStats
flowWorkspace Imports The whole set of functions/methods/classes from parent package is imported to the namespace of flowStats. 80 25
fda Imports 10 0 0 60 9
rrcov Imports 1 0 0 12 3
flowViz Imports The whole set of functions/methods/classes from parent package is imported to the namespace of flowStats. 28 3
mnormt Imports 1 0 0 0 1
corpcor Imports 1 0 0 1 1
methods Imports 5 0 3 0 0
grDevices Imports 17 0 0 0 0
graphics Imports 14 0 0 0 0
stats Imports 31 0 0 0 0
utils Imports 2 0 0 0 0
RColorBrewer Imports 1 0 0 0 0
KernSmooth Imports 1 0 0 1 0
BiocGenerics Imports 0 14 0 4 0
cluster Imports 1 0 0 4 0
MASS Imports 4 0 0 5 0
Biobase Imports 1 1 0 5 0
lattice Imports 13 0 0 5 0
flowCore Imports The whole set of functions/methods/classes from parent package is imported to the namespace of flowStats. 17 0
ncdfFlow Imports 2 0 0 19 0
ks Imports 2 0 0 22 0
testthat Suggests No object is imported into the namespace of flowStats. 36 14
openCyto Suggests No object is imported into the namespace of flowStats. 120 10
ggcyto Suggests No object is imported into the namespace of flowStats. 84 3
ggridges Suggests No object is imported into the namespace of flowStats. 40 2
xtable Suggests No object is imported into the namespace of flowStats. 2 1
graph Enhances No object is imported into the namespace of flowStats. 6 0
RBGL Enhances No object is imported into the namespace of flowStats. 8 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 flowStats Co-heaviness as Jaccard coeffcient
fda flowWorkspace 25 0.424

Analysis was done with pkgndep.