deleted file mode 100644

@@ -1,89 +0,0 @@

-#' @title Plotting function of runMusic.R

-#' @description A wrapper that plots heatmap and cluster plots for results from runMusic.R

-#' @param inSCE A \link[SingleCellExperiment]{SingleCellExperiment} object.

-#' @param analysisType Character. Specify which function to run 

-#'  Available options are  "EstCellProp","PreGroupedClustProp","SingleCellClust"

-#' @param heatmapTitle Character. Title for heatmap; Default is NULL

-#' @param analysisName Character. User-defined analysis name.

-#' This will be used as the slot name and results can be stored and retrived from SCE object using this name

-#' @return SingleCellExperiment object containing the outputs of the

-#'  specified algorithms in the \link{colData}

-#' of \code{inSCE}.

-

-library(singleCellTK)

-

-

-plotMusicResults<- function(inSCE, 

-                            analysisType = c("EstCellProp","PreGroupedClustProp","SingleCellClust"),

-                            heatmapTitle = NULL,

-                            analysisName = NULL,

-                            useAssay = NULL){

-  

-  

-  # Plot clusters

-  

-  .musicPlotclusters<- function(inSCE,analysisName){

-    basisObject = metadata(inSCE)[["sctk"]][["music"]][[analysisName]][["Disgn.mtx"]]

-    calc_dmat_dist = dist(t(log(basisObject + 1e-6)), method = "euclidean")

-    hc1<- hclust(calc_dmat_dist, method = "complete")

-    basisObject2 =  metadata(inSCE)[["sctk"]][["music"]][[analysisName]][["M.theta"]]

-    calc_RA_dist = dist(t(log(basisObject2 + 1e-8)), method = "euclidean")

-    hc2<- hclust(calc_RA_dist,method = "complete")

-    p1<-plot(hc1,cex =0.6,hang = -1, main = 'Cluster log(Design Matrix)')

-    p2<-plot(hc2,cex =0.6,hang = -1, main = 'Cluster log(Mean of RA)')

-    return(list(hc1,hc2))

-    

-  }

-  

-  

-  # plot heatmap  # use the ones from lab inSCEheatmap? (uses complexheatmap)

-  

-  .plotHeatmap<- function(inSCE, # 

-                          analysisName,

-                          heatmapTitle = NULL, 

-                          useAssay = useAssay){

-    

-    

-    

-    

-    testBulk<-metadata(inSCE)[["sctk"]][["music"]][[analysisName]][[useAssay]]

-    bulkinSCE<-SingleCellExperiment(assays = list(EstProps = testBulk))

-    names(assays(bulkinSCE))<-useAssay

-    heatmap<-plotSCEHeatmap(bulkinSCE,  # Check version

-                            useAssay = useAssay, 

-                            rowLabel = T, 

-                            colLabel = T, 

-                            rowTitle = "Subjects",

-                            colTitle = "CellType",

-                            title = heatmapTitle)

-    return(heatmap)

-  }

-  

-  # sce -> extract bulk -> new_sce -> plotsce

-  

-  

-  

-  if(analysisType == "SingleCellClust"){

-    plots<-.musicPlotclusters(inSCE,analysisName = analysisName)

-  #  metadata(inSCE)$sctk$music[[analysisName]][["Clusters"]]<- temp_results 

-  }

-  else if(analysisType == "EstCellProp"){

-    

-    plots<-.plotHeatmap(inSCE,heatmapTitle = heatmapTitle,useAssay = "Est.prop.weighted" ,analysisName = analysisName )

-    # Do if else for pulling the assay data and have one single call for the sce heatmap

-    

-    #metadata(inSCE)$sctk$music[[analysisName]][["Heatmap"]]<- temp_results 

-    

-  }

-    

-  else if(analysisType == "PreGroupedClustProp"){

-        

-    plots<- .plotHeatmap(inSCE,heatmapTitle = heatmapTitle,useAssay = "Est.prop.weighted.cluster",analysisName = analysisName )

-    #metadata(inSCE)$sctk$music[[analysisName]][["Heatmap"]]<- temp_results 

-    

-  }

-

-

-  return(plots)

-} 

-