Dependency analysis on package FlowSOM

General information

Bioconductor link link
Package version2.4.0
Number of strong dependencies187
Number of all dependencies199
Number of parent packages26
Max heaviness from parent packages45
Total heaviness from parent packages98
Number of parent packages (including Suggests and Enhances)28
Max co-heaviness from parent packages ("CytoML" and "flowWorkspace")23

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils methods grDevices stats graphics grid splines tools stats4 parallel tcltk magrittr glue R6 rlang pkgconfig lifecycle tibble vctrs pillar ellipsis fansi cli crayon utf8 digest Matrix lattice scales RColorBrewer gtable farver labeling munsell viridisLite colorspace withr MASS isoband mgcv nlme ggplot2 Rcpp tidyselect purrr generics jsonlite Biobase BiocGenerics dplyr cytolib RcppParallel BH RProtoBufLib Rhdf5lib RcppArmadillo matrixStats S4Vectors base64enc yaml evaluate cluster cpp11 RcppEigen flowCore XML data.table RBGL Rgraphviz graph xml2 latticeExtra aws.s3 aws.signature ncdfFlow DelayedArray png jpeg curl httr zlibbioc MatrixGenerics IRanges mime openssl askpass sys gridExtra stringr stringi knitr highr xfun brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 ALL tweenr polyclip ggrepel ggsci tidyr cowplot ggsignif polynom rstatix broom corrplot car backports carData abind nnet pbkrtest quantreg maptools lme4 numDeriv SparseM MatrixModels survival sp foreign boot minqa nloptr testthat flowWorkspace openCyto plyr ggcyto corpcor RUnit gtools flowViz flowStats flowClust clue ks rrcov R.utils hexbin KernSmooth IDPmisc fda mnormt FNN kernlab mclust multicool mvtnorm plot3D pracma robustbase pcaPP R.oo R.methodsS3 fds deSolve misc3d DEoptimR rainbow RCurl hdrcde bitops locfit ash bookdown rmarkdown BiocManager htmltools jquerylib tinytex bslib fastmap sass fs rappdirs 0 5 10 Imported methods 0 50 100 Required packages 0 20 40 Heaviness from parents igraph stats utils colorRamps grDevices magrittr methods RColorBrewer rlang XML BiocGenerics Rtsne ConsensusClusterPlus flowCore pheatmap dplyr tidyr ggplot2 ggnewscale ggpointdensity scattermore ggrepel ggforce flowWorkspace ggpubr CytoML BiocStyle testthat In total 187 packages are required directly or indirectly (199) when installing 'FlowSOM' (2.4.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'FlowSOM' Imported functions


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on FlowSOM
igraph Depends 12 0 0 10 1
ggpubr Imports 6 0 0 96 45
CytoML Imports 2 0 0 125 41
ggforce Imports 2 0 0 44 3
ConsensusClusterPlus Imports 1 0 0 9 2
colorRamps Imports 1 0 0 0 1
Rtsne Imports 1 0 0 4 1
pheatmap Imports 1 0 0 18 1
ggnewscale Imports 1 0 0 38 1
ggpointdensity Imports 1 0 0 38 1
scattermore Imports 1 0 0 38 1
stats Imports 8 0 0 0 0
utils Imports 1 0 0 0 0
grDevices Imports 5 0 0 0 0
magrittr Imports 1 0 0 0 0
methods Imports 1 0 0 0 0
RColorBrewer Imports 1 0 0 0 0
rlang Imports 1 0 0 1 0
XML Imports 2 0 0 2 0
BiocGenerics Imports 1 0 0 4 0
flowCore Imports 13 0 0 17 0
dplyr Imports 10 0 0 20 0
tidyr Imports 1 0 0 22 0
ggplot2 Imports 5 0 0 37 0
ggrepel Imports 1 0 0 39 0
flowWorkspace Imports 4 0 0 80 0
BiocStyle Suggests No object is imported into the namespace of FlowSOM. 30 12
testthat Suggests No object is imported into the namespace of FlowSOM. 36 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 FlowSOM Co-heaviness as Jaccard coeffcient
flowWorkspace CytoML 23 0.359

Analysis was done with pkgndep.