Creates diffusion maps


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Documentation for package ‘destiny’ version 1.0.0

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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 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
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
values DiffusionMap methods
values<- DiffusionMap methods
vectors DiffusionMap methods
vectors<- DiffusionMap methods