Creates diffusion maps


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Documentation for package ‘destiny’ version 1.2.1

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destiny-package Create and plot diffusion maps
as.data.frame-method DiffusionMap coercions
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
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 DiffusionMap methods
dataset<- DiffusionMap methods
destiny Create and plot diffusion maps
DiffusionMap Create a diffusion map of cells
DiffusionMap class Create a diffusion map of cells
DiffusionMap coercions DiffusionMap coercions
DiffusionMap methods DiffusionMap methods
DiffusionMap-class Create a diffusion map of cells
DiffusionMap-coercions DiffusionMap coercions
DiffusionMap-methods DiffusionMap methods
dm.predict Predict new data points using an existing DiffusionMap. The resulting matrix can be used in the plot method for the DiffusionMap
eigenvalues DiffusionMap methods
eigenvalues<- DiffusionMap methods
eigenvectors DiffusionMap methods
eigenvectors<- DiffusionMap methods
ExpressionSet helpers Convert object to ExpressionSet or read it from a file
find.dm.k Find a suitable k
find.sigmas Calculate the average dimensionality for m different gaussian kernel widths (sigma).
fortify.DiffusionMap DiffusionMap coercions
guo Guo at al. mouse embryonic stem cell qPCR data
guo.norm Guo at al. mouse embryonic stem cell qPCR data
lWhich Logical which
optimal.sigma Sigmas Object
optimal.sigma-method DiffusionMap methods
optimal.sigma-method Sigmas Object
plot-method 3D or 2D plot of diffusion map
plot-method Plot Sigmas object
plot.DiffusionMap 3D or 2D plot of diffusion map
plot.Sigmas Plot Sigmas object
print-method DiffusionMap methods
print-method Sigmas Object
read.ExpressionSet Convert object to ExpressionSet or read it from a file
show-method DiffusionMap methods
show-method Sigmas Object
Sigmas Sigmas Object
sigmas DiffusionMap methods
Sigmas class Sigmas Object
Sigmas-class Sigmas Object
Sigmas-methods Sigmas Object
sigmas<- DiffusionMap methods
updateObject-method Update old DiffusionMaps to a newer version
values DiffusionMap methods
values<- DiffusionMap methods
vectors DiffusionMap methods
vectors<- DiffusionMap methods