Package: destiny 3.21.0
Philipp Angerer
destiny: Creates diffusion maps
Create and plot diffusion maps.
Authors:
destiny_3.21.0.tar.gz
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destiny.pdf |destiny.html✨
destiny/json (API)
NEWS
| # Install 'destiny' in R: |
| install.packages('destiny', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/theislab/destiny/issues
On BioConductor:destiny-3.21.0(bioc 3.21)destiny-3.20.0(bioc 3.20)
cellbiologycellbasedassaysclusteringsoftwarevisualizationdiffusion-mapsdimensionality-reduction
Last updated 4 days agofrom:11ed147954. Checks:OK: 1 NOTE: 7 ERROR: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 19 2024 |
| R-4.5-win-x86_64 | NOTE | Nov 19 2024 |
| R-4.5-linux-x86_64 | NOTE | Nov 19 2024 |
| R-4.4-win-x86_64 | NOTE | Nov 19 2024 |
| R-4.4-mac-x86_64 | NOTE | Nov 19 2024 |
| R-4.4-mac-aarch64 | NOTE | Nov 19 2024 |
| R-4.3-win-x86_64 | NOTE | Nov 19 2024 |
| R-4.3-mac-x86_64 | NOTE | Nov 19 2024 |
| R-4.3-mac-aarch64 | ERROR | Nov 19 2024 |
Exports:as.data.frameas.ExpressionSetas.matrixbranch_dividecolorlegendcube_helixdatasetdataset<-DiffusionMapdistancedistance<-dm_predictDPTeig_decompeigenvalueseigenvalues<-eigenvectorseigenvectors<-featureNamesfeatureNames<-find_dm_kfind_knnfind_sigmasfind_tipsfortify.DiffusionMapfortify.DPTgene_relevancel_whichncolnrowoptimal_sigmaplotplot_differential_mapplot_gene_relevanceplot_gene_relevance_rankplot.DiffusionMapplot.DPTprintprojection_distrandom_rootread.ExpressionSetscale_color_cube_helixscale_colour_cube_helixscale_fill_cube_helixshowsigmasSigmassigmas<-tipsupdateObject
Dependencies:abindaskpassbackportsBiobaseBiocGenericsbootbroomcarcarDataclassclicolorspacecowplotcpp11crayoncurldata.tableDelayedArrayDEoptimRDerivdoBydplyre1071fansifarverFormulagenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot.multistatsggplot2ggthemesgluegtablehexbinhttrIRangesirlbaisobandjsonliteknn.covertreelabelinglaekenlatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivopensslpbkrtestpcaMethodspillarpkgconfigproxypurrrquantregR6rangerRColorBrewerRcppRcppEigenRcppHNSWrlangrobustbaseRSpectraS4ArraysS4Vectorsscalesscatterplot3dSingleCellExperimentsmootherspSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectTTRUCSC.utilsutf8vcdvctrsVIMviridisLitewithrxtsXVectorzlibbioczoo
destiny 2.0 brought the Diffusion Pseudo Time (DPT) class
Rendered fromDPT.Rmdusingknitr::rmarkdownon Nov 19 2024.Last update: 2024-10-28
Started: 2022-01-29
destiny main vignette: Start here!
Rendered fromDiffusion-Maps.Rmdusingknitr::rmarkdownon Nov 19 2024.Last update: 2024-11-13
Started: 2022-01-29
detecting relevant genes with destiny 3
Rendered fromGene-Relevance.Rmdusingknitr::rmarkdownon Nov 19 2024.Last update: 2024-11-18
Started: 2022-01-29
Reproduce the Diffusion Map vignette with the supplied data()
Rendered fromDiffusion-Map-recap.Rmdusingknitr::rmarkdownon Nov 19 2024.Last update: 2022-01-29
Started: 2022-01-29
The effects of a global vs. local kernel
Rendered fromGlobal-Sigma.Rmdusingknitr::rmarkdownon Nov 19 2024.Last update: 2024-10-28
Started: 2022-01-29
tidyverse and ggplot integration with destiny
Rendered fromtidyverse.Rmdusingknitr::rmarkdownon Nov 19 2024.Last update: 2024-10-28
Started: 2022-01-29
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 |
