CEllular Latent Dirichlet Allocation


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Documentation for package ‘celda’ version 1.0.4

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A B C D E F G L M N P R S T V

-- A --

appendCeldaList Append two celdaList objects
availableModels available models

-- B --

bestLogLikelihood Get the log-likelihood
bestLogLikelihood-method Get the log-likelihood

-- C --

celda Celda models
celdaCGGridSearchRes celdaCGGridSearchRes
celdaCGMod celdaCGmod
celdaCGSim celdaCGSim
celdaCMod celdaCMod
celdaCSim celdaCSim
celdaGMod celdaGMod
celdaGridSearch Run Celda in parallel with multiple parameters
celdaGSim celdaGSim
celdaHeatmap Plot celda Heatmap
celdaHeatmap-method Heatmap for celda_C
celdaHeatmap-method Heatmap for celda_CG
celdaHeatmap-method Heatmap for celda_CG
celdaPerplexity Get perplexity for every model in a celdaList
celdaPerplexity-method Get perplexity for every model in a celdaList
celdaProbabilityMap Renders probability and relative expression heatmaps to visualize the relationship between feature modules and cell populations.
celdaProbabilityMap-method Probability map for a celda_C model
celdaProbabilityMap-method Probability map for a celda_CG model
celdaTsne Embeds cells in two dimensions using tSNE based on celda_CG results.
celdaTsne-method tSNE for celda_C
celdaTsne-method tSNE for celda_CG
celdaTsne-method tSNE for celda_G
celdaUmap Embeds cells in two dimensions using umap.
celdaUmap-method umap for celda_C
celdaUmap-method umap for celda_CG
celdaUmap-method umap for celda_G
celda_C Cell clustering with Celda
celda_CG Cell and feature clustering with Celda
celda_G Feature clustering with Celda
clusterProbability Get cluster probability
clusterProbability-method Conditional probabilities for cells in subpopulations from a Celda_C model
clusterProbability-method Conditional probabilities for cells and features from a Celda_CG model
clusterProbability-method Conditional probabilities for features in modules from a Celda_G model
clusters Get clustering outcomes from a celdaModel
clusters-method Get clustering outcomes from a celdaModel
compareCountMatrix Check count matrix consistency
contaminationSim contaminationSim
countChecksum Get the MD5 hash of the count matrix from the celdaList
countChecksum-method Get the MD5 hash of the count matrix from the celdaList

-- D --

decontX Decontaminate count matrix
differentialExpression Differential expression for cell subpopulations using MAST
distinctColors Create a color palette

-- E --

eigenMatMultInt Fast matrix multiplication for double x int

-- F --

factorizeMatrix Generate factorized matrices showing each feature's influence on cell / gene clustering
factorizeMatrix-method Matrix factorization for results from celda_C()
factorizeMatrix-method Matrix factorization for results from celda_CG
factorizeMatrix-method Matrix factorization for results from celda_G
fastNormProp Fast normalization for numeric matrix
fastNormPropLog Fast normalization for numeric matrix
fastNormPropSqrt Fast normalization for numeric matrix
featureModuleLookup Obtain the gene module of a gene of interest
featureModuleLookup-method Lookup the module of a feature
featureModuleLookup-method Lookup the module of a feature
featureModuleLookup-method Lookup the module of a feature
featureModuleTable Outputting a feature module table

-- G --

geneSetEnrich Gene set enrichment

-- L --

logLikelihood Calculate LogLikelihood
logLikelihoodcelda_C Calculate Celda_C log likelihood
logLikelihoodcelda_CG Calculate Celda_CG log likelihood
logLikelihoodcelda_G Calculate Celda_G log likelihood
logLikelihoodHistory Get log-likelihood history
logLikelihoodHistory-method Get log-likelihood history

-- M --

matrixNames Get feature, cell and sample names from a celdaModel
matrixNames-method Get feature, cell and sample names from a celdaModel
moduleHeatmap Heatmap for featureModules

-- N --

normalizeCounts Normalization of count data

-- P --

params Get parameter values provided for celdaModel creation
params-method Get parameter values provided for celdaModel creation
perplexity Calculate the perplexity from a single celdaModel
perplexity-method Calculate the perplexity on new data with a celda_C model
perplexity-method Calculate the perplexity on new data with a celda_CG model
perplexity-method Calculate the perplexity on new data with a celda_G model
plotDimReduceCluster Plotting the cell labels on a dimensionality reduction plot
plotDimReduceFeature Plotting feature expression on a dimensionality reduction plot
plotDimReduceGrid Mapping the dimensionality reduction plot
plotDimReduceModule Plotting the Celda module probability on a dimensionality reduction plot
plotGridSearchPerplexity Visualize perplexity of a list of celda models
plotGridSearchPerplexitycelda_C Plot perplexity as a function of K from celda_C models
plotGridSearchPerplexitycelda_CG Plot perplexity as a function of K and L from celda_CG models
plotGridSearchPerplexitycelda_G Plot perplexity as a function of L from a celda_G model
plotHeatmap Plots heatmap based on Celda model

-- R --

recodeClusterY Recode feature module clusters
recodeClusterZ Recode cell cluster labels
recursiveSplitCell Recursive cell splitting
recursiveSplitModule Recursive module splitting
resamplePerplexity Calculate and visualize perplexity of all models in a celdaList, with count resampling
resList Get final celdaModels from a celdaList
resList-method Get final celdaModels from a celdaList
runParams Get run parameters provided to 'celdaGridSearch()'
runParams-method Get run parameters provided to 'celdaGridSearch()'

-- S --

sampleCells sampleCells
sampleLabel Get sampleLabels from a celdaModel
sampleLabel-method Get sampleLabels from a celdaModel
selectBestModel Select best chain within each combination of parameters
semiPheatmap A function to draw clustered heatmaps.
simulateCells Simulate count data from the celda generative models.
simulateCellscelda_C Simulate cells from the celda_C model
simulateCellscelda_CG Simulate cells from the celda_CG model
simulateCellscelda_G Simulate cells from the celda_G model
simulateContaminatedMatrix Simulate contaminated count matrix
subsetCeldaList Subset celdaList object from celdaGridSearch

-- T --

topRank Identify features with the highest influence on clustering.

-- V --

violinPlot Feature Expression Violin Plot