R Graphical Manual

Last data update: 2014.03.03

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R Release (3.2.3)
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Results 1 - 10 of 16 found.
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DiffusionMap class (Package: destiny) : Create a diffusion map of cells

The provided data can be a double matrix of expression data or a data.frame with all non-integer (double) columns being treated as expression data features (and the others ignored), or an ExpressionSet.

● Data Source: BioConductor
● Keywords:
● Alias: DiffusionMap, DiffusionMap class, DiffusionMap-class
● 0 images

DiffusionMap coercions (Package: destiny) : DiffusionMap coercions

Convert a diffusionmap to other classes

● Data Source: BioConductor
● Keywords:
● Alias: DiffusionMap coercions, DiffusionMap-coercions, as.data.frame,DiffusionMap-method, fortify.DiffusionMap
● 0 images

DiffusionMap methods (Package: destiny) : DiffusionMap methods

Get and set eigenvalues, eigenvectors, and sigma(s) of a DiffusionMap object or print information about a DiffusionMap

● Data Source: BioConductor
● Keywords:
● Alias: DiffusionMap methods, DiffusionMap-methods, dataset, dataset<-, eigenvalues, eigenvalues<-, eigenvectors, eigenvectors<-, optimal.sigma,DiffusionMap-method, print,DiffusionMap-method, show,DiffusionMap-method, sigmas, sigmas<-, values, values<-, vectors, vectors<-
● 1 images

ExpressionSet helpers (Package: destiny) : Convert object to link[Biobase]{ExpressionSet

These functions present quick waya to create ExpressionSet objects.

● Data Source: BioConductor
● Keywords:
● Alias: ExpressionSet helpers, as.ExpressionSet, as.ExpressionSet,data.frame-method, as.ExpressionSet-method, read.ExpressionSet
● 0 images

Sigmas class (Package: destiny) : Sigmas Object

Holds the information about how the sigma parameter for a DiffusionMap was obtained, and in this way provides a plotting function for the find.sigmas heuristic. You should not need to create a Sigmas object yourself. Provide sigma to DiffusionMap instead or use find.sigmas.

● Data Source: BioConductor
● Keywords:
● Alias: Sigmas, Sigmas class, Sigmas-class, Sigmas-methods, optimal.sigma, optimal.sigma,Sigmas-method, print,Sigmas-method, show,Sigmas-method
● 0 images

colorlegend (Package: destiny) : Color legend

Creates a color legend for a vector used to color a plot. It will use the current palette() or the specified pal as reference.

● Data Source: BioConductor
● Keywords:
● Alias: colorlegend
● 1 images

cube.helix (Package: destiny) : Sequential color palette using the cube helix system

Creates a perceptually monotonously decreasing (or increasing) lightness color palette with different tones.

● Data Source: BioConductor
● Keywords:
● Alias: cube.helix
● 2 images

destiny (Package: destiny) : Create and plot diffusion maps

The main function is DiffusionMap, which returns an object you can plot (plot.DiffusionMap is then called).

● Data Source: BioConductor
● Keywords:
● Alias: destiny, destiny-package
● 2 images

dm.predict (Package: destiny) : Predict new data points using an existing DiffusionMap. The resulting matrix can be used in link[=plot.DiffusionMap]{the plot method for the DiffusionMap

Predict new data points using an existing DiffusionMap. The resulting matrix can be used in the plot method for the DiffusionMap

● Data Source: BioConductor
● Keywords:
● Alias: dm.predict
● 1 images

find.dm.k (Package: destiny) : Find a suitable k

The k parameter for the k nearest neighbors used in DiffusionMap should be as big as possible while still being computationally feasible. This function approximates it depending on the size of the dataset n.

● Data Source: BioConductor
● Keywords:
● Alias: find.dm.k
● 2 images