properTy

Naive, memory, activation, effector, exhaustion properties of T cells

Install

devtools::install_github('zgyaru/properTy')

Example

Step 1. Loading example data

library(properTy)

## It is a SingleCellExperiment toy dataset
data = loadExample()

Step 2. Calculating immune property score

score = properTy(scMat = data@assays@data$counts, 
                 clusterNames = data.frame(data$clusterNames, row.names = colnames(data)))

Step 3. Visulizing immune properties of interested T subSets

DensityProp(score, 
            c('CD8+ Tex-SPRY1', 'CD8+ Tex-XAF1', 'CD8+ Tex-MKI67')   ## interested cell cluster names
            )

PieProp(score, 
        c('CD8+ Tex-SPRY1', 'CD8+ Tex-XAF1', 'CD8+ Tex-MKI67')   ## interested cell cluster names
        )