Package: destiny 3.26.0

Philipp Angerer

destiny: Creates diffusion maps

Create and plot diffusion maps.

Authors:Philipp Angerer [cre, aut], Laleh Haghverdi [ctb], Maren Büttner [ctb], Fabian Theis [ctb], Carsten Marr [ctb], Florian Büttner [ctb]

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manual.pdf |manual.html✨
card.svg |card.png
destiny/json (API)
NEWS

# Install 'destiny' in R:

install.packages('destiny', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/theislab/destiny/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

guo - Guo at al. mouse embryonic stem cell qPCR data
guo_norm - Guo at al. mouse embryonic stem cell qPCR data

On BioConductor:destiny-3.27.0(bioc 3.24)destiny-3.26.0(bioc 3.23)

cellbiology cellbasedassays clustering software visualization diffusion-maps dimensionality-reduction cpp

11.69 score 106 stars 1 packages 1.0k scripts 1.5k downloads 18 mentions 50 exports 130 dependencies

Last updated from:60f95ca31e (on RELEASE_3_23). Checks:12 NOTE, 2 OK. Indexed: no.

Target	Result	Time	Files	Syslog
bioc-checks	NOTE	331
linux-devel-arm64	NOTE	434
linux-devel-x86_64	NOTE	480
source / vignettes	OK	719
linux-release-arm64	NOTE	429
linux-release-x86_64	NOTE	488
macos-release-arm64	NOTE	341
macos-release-x86_64	NOTE	557
macos-oldrel-arm64	NOTE	255
macos-oldrel-x86_64	NOTE	507
windows-devel	NOTE	1506
windows-release	NOTE	1542
windows-oldrel	NOTE	1643
wasm-release	OK	272

Exports:as.data.frame as.ExpressionSet as.matrix branch_divide colorlegend cube_helix dataset dataset<-DiffusionMap distance distance<-dm_predict DPT eig_decomp eigenvalues eigenvalues<-eigenvectors eigenvectors<-featureNames featureNames<-find_dm_k find_knn find_sigmas find_tips fortify.DiffusionMap fortify.DPT gene_relevance l_which ncol nrow optimal_sigma plot plot_differential_map plot_gene_relevance plot_gene_relevance_rank plot.DiffusionMap plot.DPT print projection_dist random_root read.ExpressionSet scale_color_cube_helix scale_colour_cube_helix scale_fill_cube_helix show sigmas Sigmas sigmas<-tips updateObject

Dependencies:abind backports bbotk Biobase BiocGenerics boot broom car carData checkmate class cli codetools colorspace cowplot cpp11 data.table DelayedArray DEoptimR Deriv digest doBy dplyr e1071 evaluate farver forecast Formula fracdiff future future.apply generics GenomicRanges ggplot.multistats ggplot2 ggthemes globals glue gtable hexbin IRanges irlba isoband jsonlite knn.covertree labeling laeken lattice lgr lifecycle listenv lme4 lmtest magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mgcv microbenchmark minqa mirai mlbench mlr3 mlr3learners mlr3measures mlr3misc mlr3pipelines mlr3tuning modelr moocore nanonext nlme nloptr nnet numDeriv palmerpenguins paradox parallelly pbkrtest pcaMethods pillar pkgconfig proxy PRROC purrr quantreg R6 ranger rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppHNSW Rdpack reformulas rlang robustbase RSpectra S4Arrays S4Vectors S7 scales scatterplot3d Seqinfo SingleCellExperiment sp SparseArray SparseM stringi stringr SummarizedExperiment survival tibble tidyr tidyselect timeDate urca utf8 uuid vcd vctrs VIM viridisLite withr xgboost XVector zoo

destiny 2.0 brought the Diffusion Pseudo Time (DPT) class

Rendered fromDPT.Rmdusingknitr::rmarkdownon Jun 14 2026.

Last update: 2026-04-15
Started: 2022-01-29

destiny main vignette: Start here!

Rendered fromDiffusion-Maps.Rmdusingknitr::rmarkdownon Jun 14 2026.

Last update: 2026-04-15
Started: 2022-01-29

detecting relevant genes with destiny 3

Rendered fromGene-Relevance.Rmdusingknitr::rmarkdownon Jun 14 2026.

Last update: 2026-04-15
Started: 2022-01-29

Reproduce the Diffusion Map vignette with the supplied data()

Rendered fromDiffusion-Map-recap.Rmdusingknitr::rmarkdownon Jun 14 2026.

Last update: 2026-04-15
Started: 2022-01-29

The effects of a global vs. local kernel

Rendered fromGlobal-Sigma.Rmdusingknitr::rmarkdownon Jun 14 2026.

Last update: 2026-04-15
Started: 2022-01-29

tidyverse and ggplot integration with destiny

Rendered fromtidyverse.Rmdusingknitr::rmarkdownon Jun 14 2026.

Last update: 2026-04-15
Started: 2022-01-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Coercion methods	as.data.frame,DiffusionMap-method as.data.frame,DPT-method as.data.frame.DiffusionMap as.data.frame.DPT as.matrix,DPT-method as.matrix.DPT Coercion methods fortify.DiffusionMap fortify.DPT
Color legend	colorlegend
Sequential color palette using the cube helix system	cube_helix scale_color_cube_helix scale_colour_cube_helix scale_fill_cube_helix
Create and plot diffusion maps	destiny-package destiny
destiny generics	dataset dataset<- destiny generics distance distance<- eigenvalues eigenvalues<- eigenvectors eigenvectors<- optimal_sigma sigmas sigmas<-
DiffusionMap accession methods	dataset,DiffusionMap-method dataset<-,DiffusionMap-method DiffusionMap accession methods distance,DiffusionMap-method distance<-,DiffusionMap-method eigenvalues,DiffusionMap-method eigenvalues<-,DiffusionMap-method eigenvectors,DiffusionMap-method eigenvectors<-,DiffusionMap-method optimal_sigma,DiffusionMap-method sigmas,DiffusionMap-method sigmas<-,DiffusionMap-method
DiffusionMap methods	DiffusionMap methods print,DiffusionMap-method print.DiffusionMap show,DiffusionMap-method show.DiffusionMap
Create a diffusion map of cells	DiffusionMap DiffusionMap-class
Predict new data points using an existing DiffusionMap. The resulting matrix can be used in the plot method for the DiffusionMap	dm_predict
DPT Matrix methods	dim,DPT-method dim.DPT DPT matrix methods ncol,DPT-method ncol.DPT nrow,DPT-method nrow.DPT [,DPT,index,index,logicalOrMissing-method [,DPT,index,missing,logicalOrMissing-method [,DPT,missing,index,logicalOrMissing-method [,DPT,missing,missing,logicalOrMissing-method [.DPT [[,DPT,index,index-method
DPT methods	branch_divide dataset,DPT-method dataset.DPT dataset<-,DPT-method DPT methods tips
Diffusion Pseudo Time	DPT DPT-class
Fast eigen decomposition using 'eigs'	eig_decomp
Convert object to ExpressionSet or read it from a file	as.ExpressionSet as.ExpressionSet,data.frame-method ExpressionSet helper methods read.ExpressionSet
Extraction methods	$,DiffusionMap-method $,DPT-method $.DiffusionMap $.DPT Extraction methods names,DiffusionMap-method names,DPT-method names.DiffusionMap names.DPT [[,DiffusionMap,character,missing-method [[,DPT,character,missing-method [[.DiffusionMap [[.DPT
Find a suitable k	find_dm_k
kNN search	find_knn
Calculate the average dimensionality for m different gaussian kernel widths (sigma).	find_sigmas
Find tips in a DiffusionMap object	find_tips
Gene Relevance methods	dataset,GeneRelevance-method dataset.GeneRelevance dataset<-,GeneRelevance-method distance,GeneRelevance-method distance<-,GeneRelevance-method featureNames,GeneRelevance-method featureNames.GeneRelevance featureNames<-,GeneRelevance,characterOrFactor-method Gene Relevance methods print,GeneRelevance-method show,GeneRelevance-method
Gene relevances for entire data set	GeneRelevance-class gene_relevance gene_relevance,DiffusionMap,missing-method gene_relevance,matrix,dMatrixOrMatrix-method
Guo at al. mouse embryonic stem cell qPCR data	data:guo data:guo_norm guo guo_norm
Logical which	l_which
Plot gene relevance or differential map	Gene Relevance plotting plot,GeneRelevance,character-method plot,GeneRelevance,missing-method plot,GeneRelevance,numeric-method plot_differential_map plot_differential_map,DiffusionMap,missing-method plot_differential_map,GeneRelevance,missing-method plot_differential_map,matrix,matrix-method plot_gene_relevance plot_gene_relevance,DiffusionMap,missing-method plot_gene_relevance,GeneRelevance,missing-method plot_gene_relevance,matrix,matrix-method plot_gene_relevance_rank plot_gene_relevance_rank,DiffusionMap,missing-method plot_gene_relevance_rank,GeneRelevance,missing-method plot_gene_relevance_rank,matrix,matrix-method
3D or 2D plot of diffusion map	plot,DiffusionMap,missing-method plot,DiffusionMap,numeric-method plot.DiffusionMap
Plot DPT	plot,DPT,missing-method plot,DPT,numeric-method plot.DPT
Plot Sigmas object	plot,Sigmas,missing-method plot.Sigmas
Projection distance	projection_dist
Find a random root cell index	random_root
Sigmas Object	optimal_sigma,Sigmas-method print,Sigmas-method show,Sigmas-method Sigmas Sigmas-class Sigmas-methods
Update old destiny objects to a newer version.	updateObject methods updateObject,DiffusionMap-method updateObject,GeneRelevance-method updateObject,Sigmas-method updateObject.DiffusionMap updateObject.GeneRelevance updateObject.Sigmas

Usage by other packages (reverse dependencies)