Creates diffusion maps

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Documentation for package ‘destiny’ version 2.0.8

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destiny-package Create and plot diffusion maps
$-method Extraction methods
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
branch_divide DPT methods
coercions Coercion methods
colorlegend Color legend
cube_helix Sequential color palette using the cube helix system
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<- destiny generics
dataset<--method DPT methods
dataset<--method DiffusionMap accession methods
destiny Create and plot diffusion maps
destiny generics destiny generics
DiffusionMap Create a diffusion map of cells
DiffusionMap accessors DiffusionMap accession methods
DiffusionMap class Create a diffusion map of cells
DiffusionMap methods DiffusionMap methods
DiffusionMap-class Create a diffusion map of cells
DiffusionMap-methods DiffusionMap methods
dim.DPT DPT Matrix methods
distance destiny generics
distance-method DiffusionMap accession methods
distance<- destiny generics
distance<--method DiffusionMap accession 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
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 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 kernel widths (sigma).
find_tips Find tips in a DiffusionMap object
fortify.DiffusionMap Coercion methods
fortify.DPT Coercion methods
guo Guo at al. mouse embryonic stem cell qPCR data
guo_norm Guo at al. mouse embryonic stem cell qPCR data
l_which Logical which
names-method Extraction methods
names.DiffusionMap Extraction methods
names.DPT Extraction methods
ncol.DPT DPT Matrix methods
nrow.DPT DPT Matrix methods
optimal_sigma destiny generics
optimal_sigma-method DiffusionMap accession methods
optimal_sigma-method Sigmas Object
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
print-method DiffusionMap methods
print-method Sigmas Object
print.DiffusionMap DiffusionMap methods
random_root Find a random root cell index
read.ExpressionSet Convert object to ExpressionSet or read it from a file
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 Sigmas Object
show.DiffusionMap DiffusionMap methods
Sigmas Sigmas Object
sigmas destiny generics
Sigmas class Sigmas Object
Sigmas-class Sigmas Object
sigmas-method DiffusionMap accession methods
Sigmas-methods Sigmas Object
sigmas<- destiny generics
sigmas<--method DiffusionMap accession methods
tips DPT methods
updateObject-method Update old DiffusionMaps or Sigmas to a newer version
[.DPT DPT Matrix methods
[[-method Extraction methods