+
+
+
+
+
+
+
+
sce <- params$inSCE
+analysisName<-params$analysisName
+analysisType<-params$analysisType
+heatmapTitle<-params$heatmapTitle
+
results <- plotMusicResults(inSCE = sce, analysisType = analysisType, analysisName = analysisName, heatmapTitle = heatmapTitle)
+
+print(results)
+
+
# Tab for tool results
+ # cat(paste0('# Music Results', ' {.tabset} \n\n'))
+
+ # Subtab for a separate plot of the tool results
+# cat(paste0('## Heatmap \n\n'))
+# if (analysisType %in% c("EstCellProp","PreGroupedClustProp")){
+ #metadata(results)[["sctk"]][["music"]][[analysisName]][["Heatmap"]]
+# print(plots)
+ # }
+
+# if(analysisType == "SingleCellClust"){
+
+ # cat(paste0('## Clusters \n\n'))
+ # metadata(results)[["sctk"]][["music"]][[analysisName]][["clusters"]]
+ # getMusicPlots(sce,analysisName,"Clusters")
+# print(plots)
+ # }
+
+ # Final tab to display the parameters used
+ #cat(paste0('## Parameters \n\n'))
+ #print(params)
+
+
+
Single cell deconvolution using MuSiC, Bulk RNAseq data, Name for the
+deconvolution analysis, this will be used to store and access results
+and plots, Steps of music deconvolution
+c(EstCellProp,PreGroupedClustProp,SingleCellClust), deafult
+is NULL vector or list of gene names, default as NULL. If NULL, use all
+genes that provided by both bulk and single cell dataset, default is
+cellType character, the colData of single cell dataset used as clusters,
+default is sampleID character,the colData of single cell dataset used as
+samples, pre grouped cluster list, list of group marker, roups passes
+the column name of higher-cluster in phenoData, vector of cell types,
+default as NULL. If NULL, then use all cell types provided by single
+cell dataset, data.frame of cell sizes. 1st column contains the names of
+cell types, 2nd column has the cell sizes per cell type. Default as
+NULL. If NULL, then estimate cell size from data, logical. If TRUE, use
+the covariance across cell types, logical, default as TRUE, numeric,
+maximum iteration number, default 1000, regulation parameter, take care
+of weight when taking reciprocal, default 1e-04, Threshold of
+convergence, default 0.01, logic, subtract avg of Y and D, logical,
+divide Y and D by their standard deviation, default FALSE, logical,
+default as TRUE. If true, remove all gene with zero expression
+
+
+
+
+
+
