destiny: Creates diffusion maps
Version 2.4.0

Create and plot diffusion maps.

Browse man pages Browse package API and functions Browse package files

AuthorPhilipp Angerer [cre, aut], Laleh Haghverdi [ctb], Maren Büttner [ctb], Fabian Theis [ctb], Carsten Marr [ctb], Florian Büttner [ctb]
Bioconductor views CellBasedAssays CellBiology Clustering Software Visualization
Date of publicationNone
MaintainerPhilipp Angerer <philipp.angerer@helmholtz-muenchen.de>
LicenseGPL
Version2.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("destiny")

Man pages

coercions: Coercion methods
colorlegend: Color legend
cube_helix: Sequential color palette using the cube helix system
destiny: Create and plot diffusion maps
destiny-deprecated: Compatibility versions of functions for destiny 1.x scripts
destiny-generics: destiny generics
DiffusionMap-accessors: DiffusionMap accession methods
DiffusionMap-class: Create a diffusion map of cells
DiffusionMap-methods: DiffusionMap methods
dm_predict: Predict new data points using an existing DiffusionMap. The...
DPT: Diffusion Pseudo Time
DPT-matrix-methods: DPT Matrix methods
DPT-methods: DPT methods
eig_decomp: Fast eigen decomposition using ARPACK
ExpressionSet-helpers: Convert object to ExpressionSet or read it from a file
extractions: Extraction methods
find_dm_k: Find a suitable k
find_sigmas: Calculate the average dimensionality for m different gaussian...
find_tips: Find tips in a DiffusionMap object
Gene-Relevance: Gene relevances for entire data set
Gene-Relevance-plotting: Plot gene relevance or gradient map
guo: Guo at al. mouse embryonic stem cell qPCR data
l_which: Logical which
plot.DiffusionMap: 3D or 2D plot of diffusion map
plot.DPT: Plot DPT
plot.Sigmas: Plot Sigmas object
projection_dist: Projection distance
random_root: Find a random root cell index
Sigmas-class: Sigmas Object
updateObject-method: Update old DiffusionMaps or Sigmas to a newer version

Functions

$,DPT-method Man page
$,DiffusionMap-method Man page
DPT Man page Source code
DPT matrix methods Man page
DPT methods Man page
DPT-class Man page
DiffusionMap Man page Source code
DiffusionMap accessors Man page
DiffusionMap class Man page
DiffusionMap methods Man page
DiffusionMap-class Man page
DiffusionMap-methods Man page
DiffusionMapCompat Man page Source code
ExpressionSet helpers Man page
Gene Relevance Man page
Gene Relevance plotting Man page
GeneRelevance Man page
GeneRelevance-class Man page
Sigmas Man page
Sigmas class Man page
Sigmas-class Man page
Sigmas-methods Man page
[,DPT,index,index,logicalOrMissing-method Man page
[,DPT,index,missing,logicalOrMissing-method Man page
[,DPT,missing,index,logicalOrMissing-method Man page
[,DPT,missing,missing,logicalOrMissing-method Man page
[.DPT Man page
[[,DPT,character,missing-method Man page
[[,DPT,index,index-method Man page
[[,DiffusionMap,character,missing-method Man page
accumulated_transitions Source code
as.ExpressionSet Man page
as.ExpressionSet,data.frame-method Man page
as.ExpressionSet-method Man page
as.Matrix.dist Source code
as.data.frame,DPT-method Man page
as.data.frame,DiffusionMap-method Man page
as.data.frame.DPT Man page
as.data.frame.DiffusionMap Man page
as.matrix,DPT-method Man page
as.matrix.DPT Man page
auto_branch Source code
average_path Source code
branch_divide Man page Source code
branchcut Source code
censoring Source code
censoring_impl Source code
centered_cosine_dist Source code
check_dpt Source code
coercions Man page
colorlegend Man page Source code
continuous_colors Source code
cube.helix Man page Source code
cube_helix Man page Source code
cut_branches Source code
data:guo Man page
data:guo_norm Man page
dataset Man page
dataset,DPT-method Man page
dataset,DiffusionMap-method Man page
dataset<- Man page
dataset<-,DPT-method Man page
dataset<-,DiffusionMap-method Man page
decomp_transitions Source code
destiny Man page
destiny generics Man page
destiny-deprecated Man page
destiny-package Man page
dim,DPT-method Man page
dim.DPT Man page
distance Man page
distance,DiffusionMap-method Man page
distance<- Man page
distance<-,DiffusionMap-method Man page
dm.predict Man page Source code
dm_predict Man page Source code
dpt_for_branch Source code
dummy_dpt Source code
eig.decomp Man page Source code
eig_decomp Man page Source code
eigenvalues Man page
eigenvalues,DiffusionMap-method Man page
eigenvalues<- Man page
eigenvalues<-,DiffusionMap-method Man page
eigenvectors Man page
eigenvectors,DiffusionMap-method Man page
eigenvectors<- Man page
eigenvectors<-,DiffusionMap-method Man page
emptyplot Source code
extract_col Source code
extract_doublematrix Source code
extractions Man page
find.dm.k Man page Source code
find.sigmas Man page Source code
find_dm_k Man page Source code
find_knn Source code
find_sigmas Man page Source code
find_tips Man page Source code
flipped_dcs Source code
fortify.DPT Man page Source code
fortify.DiffusionMap Man page Source code
gene_relevance Man page
gene_relevance,DiffusionMap,missing-method Man page
gene_relevance,matrix,matrix-method Man page
gene_relevance_impl Source code
get_dimension_names Source code
get_norm_p Source code
get_plot_fn Source code
get_sigmas Source code
guo Man page
guo_norm Man page
hasattr Source code
icor2_no_censor Source code
idx_list_to_vec Source code
is_distmatrix Source code
kendall_finite_cor Source code
lWhich Man page Source code
l_which Man page Source code
n_features Source code
n_samples Source code
names,DPT-method Man page
names,DiffusionMap-method Man page
names.DPT Man page
names.DiffusionMap Man page
ncol,DPT-method Man page
ncol.DPT Man page
no_censoring Source code
no_censoring_icor_rank Source code
nrow,DPT-method Man page
nrow.DPT Man page
onLoad Source code
optimal.sigma Man page Source code
optimal_sigma Man page
optimal_sigma,DiffusionMap-method Man page
optimal_sigma,Sigmas-method Man page
organize_branches Source code
plot,DPT,missing-method Man page
plot,DPT,numeric-method Man page
plot,DiffusionMap,missing-method Man page
plot,DiffusionMap,numeric-method Man page
plot,GeneRelevance,character-method Man page
plot,GeneRelevance,missing-method Man page
plot,GeneRelevance,numeric-method Man page
plot,Sigmas,missing-method Man page
plot.DPT Man page Source code
plot.DiffusionMap Man page Source code
plot.GeneRelevance Man page
plot.Sigmas Man page
plot_gene_relevance Man page
plot_gene_relevance,DiffusionMap,missing-method Man page
plot_gene_relevance,GeneRelevance,missing-method Man page
plot_gene_relevance,matrix,matrix-method Man page
plot_gene_relevance_impl Source code
plot_gradient_map Man page
plot_gradient_map,DiffusionMap,missing-method Man page
plot_gradient_map,GeneRelevance,missing-method Man page
plot_gradient_map,matrix,matrix-method Man page
plot_gradient_map_impl Source code
predict_censoring Source code
predict_censoring_impl Source code
print,DiffusionMap-method Man page
print,Sigmas-method Man page
print.DiffusionMap Man page
projection_dist Man page Source code
random_root Man page Source code
rankcor_dist Source code
read.ExpressionSet Man page Source code
rescale_mat Source code
scale_color_cube_helix Man page
scale_colour_cube_helix Man page Source code
scale_cube_helix Source code
scale_fill_cube_helix Man page Source code
set_palette Source code
show,DiffusionMap-method Man page
show,Sigmas-method Man page
show.DiffusionMap Man page
sigma_msg Source code
sigmas Man page
sigmas,DiffusionMap-method Man page
sigmas<- Man page
sigmas<-,DiffusionMap-method Man page
stopifnot_distmatrix Source code
stopifsmall Source code
test_censoring Source code
tips Man page Source code
tipstats Source code
transition_probabilities Source code
updateObject,DiffusionMap-method Man page
updateObject,Sigmas-method Man page
updateObject-method Man page
update_slot_names Source code
validate_censoring Source code
verbose_timing Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/RcppExports.R
R/aaa.r
R/accessor-generics.r
R/censoring.r
R/colorlegend.r
R/compat.r
R/cube_helix.r
R/destiny-package.r
R/diffusionmap-methods-accession.r
R/diffusionmap-methods.r
R/diffusionmap-plotting.r
R/diffusionmap.r
R/dist-matrix-coerce.r
R/dpt-branching.r
R/dpt-helpers.r
R/dpt-methods-matrix.r
R/dpt-methods.r
R/dpt-plotting.r
R/dpt.r
R/eig_decomp.r
R/expressionset-helpers.r
R/find_dm_k.r
R/gene-relevance-plotting.r
R/gene-relevance.r
R/guo-data.r
R/l_which.r
R/methods-coercion.r
R/methods-extraction.r
R/methods-update.r
R/plothelpers.r
R/predict.r
R/projection-dist.r
R/s4-unions.r
R/sigmas-plotting.r
R/sigmas.r
R/utils.r
build
build/vignette.rds
data
data/guo.rda
data/guo_norm.rda
demo
demo/00Index
demo/destiny.r
inst
inst/CITATION
inst/doc
inst/doc/DPT.ipynb
inst/doc/DPT.ipynbmeta
inst/doc/DPT.pdf
inst/doc/DPT.r
inst/doc/Diffusion-Map-recap.ipynb
inst/doc/Diffusion-Map-recap.ipynbmeta
inst/doc/Diffusion-Map-recap.pdf
inst/doc/Diffusion-Map-recap.r
inst/doc/Diffusion-Maps.ipynb
inst/doc/Diffusion-Maps.ipynbmeta
inst/doc/Diffusion-Maps.pdf
inst/doc/Diffusion-Maps.r
inst/doc/Global-Sigma.ipynb
inst/doc/Global-Sigma.ipynbmeta
inst/doc/Global-Sigma.pdf
inst/doc/Global-Sigma.r
inst/doc/bibliography.bib
inst/doc/destiny-base.tplx
inst/doc/destiny-bib.tplx
inst/doc/destiny.tplx
inst/doc/destiny_processors.py
man
man/DPT-matrix-methods.Rd
man/DPT-methods.Rd
man/DPT.Rd
man/DiffusionMap-accessors.Rd
man/DiffusionMap-class.Rd
man/DiffusionMap-methods.Rd
man/ExpressionSet-helpers.Rd
man/Gene-Relevance-plotting.Rd
man/Gene-Relevance.Rd
man/Sigmas-class.Rd
man/coercions.Rd
man/colorlegend.Rd
man/cube_helix.Rd
man/destiny-deprecated.Rd
man/destiny-generics.Rd
man/destiny.Rd
man/dm_predict.Rd
man/eig_decomp.Rd
man/extractions.Rd
man/find_dm_k.Rd
man/find_sigmas.Rd
man/find_tips.Rd
man/guo.Rd
man/l_which.Rd
man/plot.DPT.Rd
man/plot.DiffusionMap.Rd
man/plot.Sigmas.Rd
man/projection_dist.Rd
man/random_root.Rd
man/updateObject-method.Rd
src
src/Makevars
src/RcppExports.cpp
src/censoring.cpp
src/no_censoring.cpp
tests
tests/testthat
tests/testthat.R
tests/testthat/test_distances.r
vignettes
vignettes/DPT.ipynb
vignettes/DPT.ipynbmeta
vignettes/Diffusion-Map-recap.ipynb
vignettes/Diffusion-Map-recap.ipynbmeta
vignettes/Diffusion-Maps.ipynb
vignettes/Diffusion-Maps.ipynbmeta
vignettes/Global-Sigma.ipynb
vignettes/Global-Sigma.ipynbmeta
vignettes/bibliography.bib
vignettes/destiny-base.tplx
vignettes/destiny-bib.tplx
vignettes/destiny.tplx
vignettes/destiny_processors.py
vignettes/mmc4.xls
vignettes/mmc6.xls
destiny documentation built on May 20, 2017, 10:35 p.m.