shinyInput-ClusterInput-method: prepare Shiny input
In JuanXie19/TCRlineageClust:

Description Usage Arguments Details Value Examples

This function prepares the input for the shiny app

1 2	## S4 method for signature 'ClusterInput' shinyInput(ClusterInput)

object

A ClusterInput object

This function takes the ClusterInputobject as the input and turns it into a dataframe that can be directly used as input of our shiny app. The shiny app allows users to intuitively investigate how the clustering tuning parameters affect clustering results

A data frame with cell clonotype and UMAP coordinates .

TCR <-read.csv("/PATH/TO/YOUR/scTCR-seqData/",header=T)
load('Mice.sub.rda')
Combined <- getCombinedDataSet(TCR,Mice.sub)
Trajectory <- getClonotyoeLineages(Combined,start.clus = NULL, end.clus = NULL, dist.method = 'simple', use.median = TRUE)
clustInput <- getClusteringInput(Trajectory)
shinyInput <- shinyInput(clustInput)
write.csv(shinyInput,file='/path/to/folder/shiny.csv')