Creates diffusion maps

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Documentation for package ‘destiny’ version 3.23.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Code demos. Use demo() to run them.
• Package NEWS.

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A B C D E F G L N O P R S T U misc

destiny-package

Create and plot diffusion maps

-- A --

as.data.frame-method	Coercion methods
as.data.frame.DiffusionMap	Coercion methods
as.data.frame.DPT	Coercion methods
as.ExpressionSet	Convert object to ExpressionSet or read it from a file
as.ExpressionSet-method	Convert object to ExpressionSet or read it from a file
as.matrix-method	Coercion methods
as.matrix.DPT	Coercion methods

-- B --

branch_divide

DPT methods

-- C --

Coercion methods	Coercion methods
colorlegend	Color legend
cube_helix	Sequential color palette using the cube helix system

-- D --

data:guo	Guo at al. mouse embryonic stem cell qPCR data
data:guo_norm	Guo at al. mouse embryonic stem cell qPCR data
dataset	destiny generics
dataset-method	DPT methods
dataset-method	DiffusionMap accession methods
dataset-method	Gene Relevance methods
dataset.DPT	DPT methods
dataset.GeneRelevance	Gene Relevance methods
dataset<-	destiny generics
dataset<--method	DPT methods
dataset<--method	DiffusionMap accession methods
dataset<--method	Gene Relevance methods
destiny	Create and plot diffusion maps
destiny generics	destiny generics
DiffusionMap	Create a diffusion map of cells
DiffusionMap accession methods	DiffusionMap accession methods
DiffusionMap methods	DiffusionMap methods
DiffusionMap-class	Create a diffusion map of cells
dim-method	DPT Matrix methods
dim.DPT	DPT Matrix methods
distance	destiny generics
distance-method	DiffusionMap accession methods
distance-method	Gene Relevance methods
distance<-	destiny generics
distance<--method	DiffusionMap accession methods
distance<--method	Gene Relevance methods
dm_predict	Predict new data points using an existing DiffusionMap. The resulting matrix can be used in the plot method for the DiffusionMap
DPT	Diffusion Pseudo Time
DPT matrix methods	DPT Matrix methods
DPT methods	DPT methods
DPT-class	Diffusion Pseudo Time

-- E --

eigenvalues	destiny generics
eigenvalues-method	DiffusionMap accession methods
eigenvalues<-	destiny generics
eigenvalues<--method	DiffusionMap accession methods
eigenvectors	destiny generics
eigenvectors-method	DiffusionMap accession methods
eigenvectors<-	destiny generics
eigenvectors<--method	DiffusionMap accession methods
eig_decomp	Fast eigen decomposition using 'eigs'
ExpressionSet helper methods	Convert object to ExpressionSet or read it from a file
Extraction methods	Extraction methods

-- F --

featureNames-method	Gene Relevance methods
featureNames.GeneRelevance	Gene Relevance methods
featureNames<--method	Gene Relevance methods
find_dm_k	Find a suitable k
find_knn	kNN search
find_sigmas	Calculate the average dimensionality for m different gaussian kernel widths (sigma).
find_tips	Find tips in a DiffusionMap object
fortify.DiffusionMap	Coercion methods
fortify.DPT	Coercion methods

-- G --

Gene Relevance methods	Gene Relevance methods
Gene Relevance plotting	Plot gene relevance or differential map
GeneRelevance-class	Gene relevances for entire data set
gene_relevance	Gene relevances for entire data set
gene_relevance-method	Gene relevances for entire data set
guo	Guo at al. mouse embryonic stem cell qPCR data
guo_norm	Guo at al. mouse embryonic stem cell qPCR data

-- L --

l_which

Logical which

-- N --

names-method	Extraction methods
names.DiffusionMap	Extraction methods
names.DPT	Extraction methods
ncol-method	DPT Matrix methods
ncol.DPT	DPT Matrix methods
nrow-method	DPT Matrix methods
nrow.DPT	DPT Matrix methods

-- O --

optimal_sigma	destiny generics
optimal_sigma-method	DiffusionMap accession methods
optimal_sigma-method	Sigmas Object

-- P --

plot-method	Plot gene relevance or differential map
plot-method	Plot DPT
plot-method	3D or 2D plot of diffusion map
plot-method	Plot Sigmas object
plot.DiffusionMap	3D or 2D plot of diffusion map
plot.DPT	Plot DPT
plot.Sigmas	Plot Sigmas object
plot_differential_map	Plot gene relevance or differential map
plot_differential_map-method	Plot gene relevance or differential map
plot_gene_relevance	Plot gene relevance or differential map
plot_gene_relevance-method	Plot gene relevance or differential map
plot_gene_relevance_rank	Plot gene relevance or differential map
plot_gene_relevance_rank-method	Plot gene relevance or differential map
print-method	DiffusionMap methods
print-method	Gene Relevance methods
print-method	Sigmas Object
print.DiffusionMap	DiffusionMap methods
projection_dist	Projection distance

-- R --

random_root	Find a random root cell index
read.ExpressionSet	Convert object to ExpressionSet or read it from a file

-- S --

scale_color_cube_helix	Sequential color palette using the cube helix system
scale_colour_cube_helix	Sequential color palette using the cube helix system
scale_fill_cube_helix	Sequential color palette using the cube helix system
show-method	DiffusionMap methods
show-method	Gene Relevance methods
show-method	Sigmas Object
show.DiffusionMap	DiffusionMap methods
Sigmas	Sigmas Object
sigmas	destiny generics
Sigmas-class	Sigmas Object
sigmas-method	DiffusionMap accession methods
Sigmas-methods	Sigmas Object
sigmas<-	destiny generics
sigmas<--method	DiffusionMap accession methods

-- T --

tips	DPT methods

-- U --

updateObject methods	Update old destiny objects to a newer version.
updateObject-method	Update old destiny objects to a newer version.
updateObject.DiffusionMap	Update old destiny objects to a newer version.
updateObject.GeneRelevance	Update old destiny objects to a newer version.
updateObject.Sigmas	Update old destiny objects to a newer version.

-- misc --

$-method	Extraction methods
$.DiffusionMap	Extraction methods
$.DPT	Extraction methods
[-method	DPT Matrix methods
[.DPT	DPT Matrix methods
[[-method	DPT Matrix methods
[[-method	Extraction methods
[[.DiffusionMap	Extraction methods
[[.DPT	Extraction methods