# Phenotypic EMD for comparison of single-cell samples

## Documentation for package ‘phemd’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

aggregateSamples | Aggregate expression data from all samples
all_expn_data | Single-cell RNA-seq expression data for melanoma samples
all_genes | All genes included in (subsampled) melanoma single-cell RNA-seq expression data
assignCellClusterNearestNode | Assign cells to a reference cell subtype
batchIDs | Accessor function for batch ID for each sample
batchIDs<- | Setter function for protein / gene markers
batchIDs<--method | Setter function for protein / gene markers
bindSeuratObj | Attach 'Seurat' object to 'Phemd' object
celltypeFreqs | Accessor function for cell subtype distribution for each sample
celltypeFreqs<- | Setter function for protein / gene markers
celltypeFreqs<--method | Setter function for protein / gene markers
clusterIndividualSamples | Computes cell subtype abundances for each sample
compareSamples | Computes EMD distance matrix representing pairwise dissimilarity between samples
createDataObj | Create 'Phemd' object
drawColnames45 | Rotates heatmap marker labels 45 degrees
embedCells | Generate cell-state embedding
gaussianffLocal | Models expression data using generalized linear model with Gaussian error
GDM | Accessor function for EMD ground distance matrix
GDM<- | Setter function for protein / gene markers
GDM<--method | Setter function for protein / gene markers
generateGDM | Computes ground distance matrix based on cell embedding
getArithmeticCentroids | Get arithmetic centroids (coordinates)
getCellYield | Gets cell yield of each sample as a table
getSampleCelltypeFreqs | Returns cell subtype distribution for each sample as a table
getSampleHistsByCluster | Gets cell subtype frequency histograms for each sample by cluster ID
getSampleSizes | Retrieve single-cell sample sizes
groupSamples | Performs community detection on sample-sample distance matrix to identify groups of similar samples
heatmap_genes | Genes to be used when plotting heatmap for melanoma single-cell RNA-seq expression data
identifyCentroids | Identify cluster centroids (cell names)
monocleInfo | Accessor function for stored Monocle object
monocleInfo<- | Setter function for protein / gene markers
monocleInfo<--method | Setter function for protein / gene markers
orderCellsMonocle | Compute Monocle2 cell state and pseudotime assignments
phateInfo | Accessor function for stored phate object
phateInfo<- | Setter function for protein / gene markers
phateInfo<--method | Setter function for protein / gene markers
Phemd | Phemd class
Phemd-class | Phemd class
Phemd-method | Setter function for protein / gene markers
Phemd-methods | Setter function for protein / gene markers
plotCellYield | Plot cell yield of each sample as bar plot
plotEmbeddings | Plots Monocle2 cell embedding plots
plotGroupedSamplesDmap | Plot diffusion map embedding of samples based on distance matrix
plotHeatmaps | Plot heatmap of cell subtypes
plotSummaryHistograms | Plots cell subtype frequency histograms summarizing each group of samples
pooledCells | Accessor function for aggregated cells used for cell subtype definition
pooledCells<- | Setter function for protein / gene markers
pooledCells<--method | Setter function for protein / gene markers
printClusterAssignments | Writes samples to file based on community detection group assignments
rawExpn | Accessor function for stored multi-sample raw expression data
rawExpn<- | Setter function for protein / gene markers
rawExpn<--method | Setter function for protein / gene markers
removeTinySamples | Remove samples with too few cells
retrieveRefClusters | Retrieve reference cell clusters
selected_genes | Genes to be used when performing clustering and trajectory analyses on melanoma single-cell RNA-seq expression data
selectFeatures | Perform feature selection on aggregated data
selectMarkers | Accessor function for gene/protein markers measured in experiment
selectMarkers<- | Setter function for protein / gene markers
selectMarkers<--method | Setter function for protein / gene markers
seuratInfo | Accessor function for stored Seurat object within Phemd object
seuratInfo<- | Setter function for protein / gene markers
seuratInfo<--method | Setter function for protein / gene markers
sNames | Accessor function for identifiers of all single-cell samples in experiment
snames_data | Sample names for melanoma single-cell RNA-seq expression data
subsampledBool | Accessor function for whether or not cells were subsampled when aggregated for cell subtype analysis
subsampledBool<- | Setter function for protein / gene markers
subsampledBool<--method | Setter function for protein / gene markers
subsampledIdx | Accessor function for aggregated cells used for cell subtype definition
subsampledIdx<- | Setter function for protein / gene markers
subsampledIdx<--method | Setter function for protein / gene markers