R/percentevent.R

In athrom/CytobankAPIstats: Computes Signaling and Population Stats for Cytometry Data on Cytobank using 'CytobankAPI'

#' Calculates the percentage of cell populations given an experiment
#It takes an API validation  key (cyto_session), 
#a list of populations of interest to calculate percentages for (popsofinterest); the reference 
#population should be listed first e.g. Live for percent of live PBMCs
#an experiment ID number for the Cytobank experiment of interest (exptID),
#a list of indices corresponding to samples from the same donor ex list(c(1,2),c(3,4,5)) if rows 1 and 2 are from pt1,3,4,5 are from pt2, etc.(grouping)
#It takes a list of specimen names as strings (specimennames)identifying the groups. This list should be the same length as grouping
#It also take a boolean (mean),if mean =TRUE, a mean for all groups in the variable group  is calculated.
#' @param cyto_session - API authentication token for session
#' @param markersofinterest - List of names of channel parameters in Cytobank
#' @param popsofinterest - List of populations of interest to calculate percentages with reference population for percentages listed first
#' @param exptID - Integer representing an experiment ID on Cytobank account
#' @param grouping - A list of indices corresponding to samples from the same donor ex list(c(1,2),c(3,4,5)) if rows 1 and 2 are from pt1,3,4,5 are from pt2, etc.
#' @param specimennames - List of specimen names as strings; needs to be same length as number of groupings
#' @param means - A boolean if mean =TRUE, a mean for all groups in the variable group  is calculated, otherwise individual means are returned.
#' @return- Returns either the percentage or mean percentage per specimen of each cell type, as specified by mean parameter
#' @examples \donttest{
#' library(CytobankAPI)
#' cyto_session <- authenticate(site="premium", username="myusername", password="mypassword")
#' markersofinterest<-c("CD3","CD56")
#' popsofinterest<-c("CD4 T cells","NK cells")
#' exptID=4
#' grouping<-list(c(1,2),c(3,4,5),c(6,7))
#' specimennames<-c("Patient1","Patient2","Control1")
#' means=T
#' percentevent(cyto_session,markersofinterest,popsofinterest,exptID,grouping,specimennames,means)
#' }
#' @export
percentevent<-function(cyto_session,markersofinterest,popsofinterest,exptID,grouping,specimennames,means){
  eventcounts<-analyzedata(cyto_session = cyto_session,markersofinterest = markersofinterest,popsofinterest =popsofinterest ,exptID=exptID,type=TRUE)
  colnames(eventcounts)=popsofinterest
  perevent=calcperevent(eventcounts)
  if(means==TRUE){
    perevent[,2:length(perevent[1,])]
    meanpercent<-apply(perevent[grouping[[1]],],2,mean)
    for (m in 2:length(grouping)){
      meanpercent<-cbind(meanpercent,apply(perevent[grouping[[m]],],2,mean))
    }
    colnames(meanpercent)<-specimennames
  }else{
    meanpercent=perevent
  }
  return(meanpercent)
}