# Creates diffusion maps

## Documentation for package ‘destiny’ version 3.1.0

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

## Help Pages

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