Creates diffusion maps


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Documentation for package ‘destiny’ version 3.23.0

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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