All functions

`[`(<DPT>,<index>,<index>,<logicalOrMissing>) `[`(<DPT>,<index>,<missing>,<logicalOrMissing>) `[`(<DPT>,<missing>,<index>,<logicalOrMissing>) `[`(<DPT>,<missing>,<missing>,<logicalOrMissing>) `[[`(<DPT>,<index>,<index>) nrow(<DPT>) ncol(<DPT>) dim(<DPT>)

DPT Matrix methods

branch_divide() tips() dataset(<DPT>) `dataset<-`(<DPT>)

DPT methods

DPT()

Diffusion Pseudo Time

eigenvalues(<DiffusionMap>) `eigenvalues<-`(<DiffusionMap>) eigenvectors(<DiffusionMap>) `eigenvectors<-`(<DiffusionMap>) sigmas(<DiffusionMap>) `sigmas<-`(<DiffusionMap>) dataset(<DiffusionMap>) `dataset<-`(<DiffusionMap>) distance(<DiffusionMap>) `distance<-`(<DiffusionMap>) optimal_sigma(<DiffusionMap>)

DiffusionMap accession methods

DiffusionMap()

Create a diffusion map of cells

print(<DiffusionMap>) show(<DiffusionMap>)

DiffusionMap methods

as.ExpressionSet() read.ExpressionSet()

Convert object to ExpressionSet or read it from a file

featureNames(<GeneRelevance>) `featureNames<-`(<GeneRelevance>,<characterOrFactor>) dataset(<GeneRelevance>) `dataset<-`(<GeneRelevance>)

Gene Relevance methods

plot_differential_map() plot_gene_relevance() plot(<GeneRelevance>,<character>) plot(<GeneRelevance>,<numeric>) plot(<GeneRelevance>,<missing>)

Plot gene relevance or differential map

gene_relevance()

Gene relevances for entire data set

Sigmas() optimal_sigma(<Sigmas>) print(<Sigmas>) show(<Sigmas>)

Sigmas Object

as.data.frame(<DiffusionMap>) fortify.DiffusionMap() as.data.frame(<DPT>) fortify.DPT() as.matrix(<DPT>)

Coercion methods

colorlegend()

Color legend

cube_helix() scale_colour_cube_helix() scale_color_cube_helix() scale_fill_cube_helix()

Sequential color palette using the cube helix system

eigenvalues() `eigenvalues<-`() eigenvectors() `eigenvectors<-`() sigmas() `sigmas<-`() dataset() `dataset<-`() distance() `distance<-`() optimal_sigma()

destiny generics

destiny

Create and plot diffusion maps

dm_predict()

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

eig_decomp()

Fast eigen decomposition using eigs

names(<DiffusionMap>) names(<DPT>) `[[`(<DiffusionMap>,<character>,<missing>) `[[`(<DPT>,<character>,<missing>) `$`(<DiffusionMap>) `$`(<DPT>)

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

guo guo_norm

Guo at al. mouse embryonic stem cell qPCR data

find_knn()

kNN search

l_which()

Logical which

plot.DPT() plot(<DPT>,<numeric>) plot(<DPT>,<missing>)

Plot DPT

plot.DiffusionMap() plot(<DiffusionMap>,<numeric>) plot(<DiffusionMap>,<missing>)

3D or 2D plot of diffusion map

plot(<Sigmas>,<missing>)

Plot Sigmas object

projection_dist()

Projection distance

random_root()

Find a random root cell index

updateObject(<DiffusionMap>) updateObject(<Sigmas>) updateObject(<GeneRelevance>)

Update old destiny objects to a newer version.