plotMusicResults update with bioC check fixes

.Rbuildignore

@@ -3,5 +3,5 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
-^SingleCellTKPlus\.Rproj$
+^singleCellTKPlus\.Rproj$
 ^\.github$

.github/workflows/BioC-check.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [master, devel]
+    branches: [main, devel]
   pull_request:
-    branches: [master, devel]
+    branches: [main, devel]
 
 name: BioC-check
 
@@ -29,7 +29,7 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v1
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}

.github/workflows/R-CMD-check.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [master, devel]
+    branches: [main, devel]
   pull_request:
-    branches: [master, devel]
+    branches: [main, devel]
 
 name: R-CMD-check
 
@@ -57,7 +57,7 @@ jobs:
           which python
         shell: bash
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
@@ -71,7 +71,7 @@ jobs:
         if: runner.os == 'macOS'
         run: brew install fftw
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: rcmdcheck
 

.gitignore

@@ -41,3 +41,9 @@ vignettes/*.pdf
 # R Environment Variables
 .Renviron
 .Rproj.user
+
+# proj env
+
+singleCellTK.Rproj
+
+

DESCRIPTION

@@ -4,18 +4,36 @@ Version: 0.0.0.9000
 Authors@R: 
     c(person(given ="Amulya", family = "Shastry", email = "shastrya@bu.edu", role = c("aut", "cre")), person(given=c("Joshua", "David"), family="Campbell", email="camp@bu.edu", role=c("aut")))
 Depends:
-    R (>= 4.0),
+    R (>= 4.2.0),
     SummarizedExperiment,
     SingleCellExperiment,
-    DelayedArray,
     Biobase,
     singleCellTK,
     ggplot2,
     dplyr,
     MuSiC,
-    magrittr
-Description: Deconvolution of bulk data from single cell datasets by MuSiC tool using singleCellTKExtra package
+    TOAST,
+    magrittr,
+    tibble,
+    S4Vectors,
+    tidyr
+Suggests:
+    testthat
+Description: "The Single Cell Toolkit (SCTK) in the singleCellTK package provides an interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. The singleCellTKPlus package adds functionality to the singleCellTK ecosystem by incorporating tools that are not installable from CRAN, Bioconductor, or Python. These tools are generally located in GitHub repositories and can be installed with "remotes". The Shiny graphical user interface (GUI) in singleCellTK will check for the installation of singleCellTKPlus and, if available, will make these tools available for use."
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
+Remotes: xuranw/MuSiC
+LazyData: FALSE
+Imports: 
+    methods,
+    rlang,
+    rmarkdown
+Collate: 
+    'data.R'
+    'descriptions.R'
+    'plotMusicResults.R'
+    'reportMusic.R'
+    'runMusic.R'
+    'utils-pipe.R'

LICENSE

@@ -1,2 +1,23 @@
+# MIT License
+
+Copyright (c) 2022 singleCellTKPlus authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
 YEAR: 2022
-COPYRIGHT HOLDER: SingleCellTKPlus authors
+COPYRIGHT HOLDER: singleCellTKPlus authors

NAMESPACE

@@ -1,9 +1,22 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
-export()
 export(description_runMusic)
 export(getMusicResults)
+export(plotMusicResults)
 export(reportMusic)
+export(reportMusicAll)
+export(reportMusicResults)
 export(runMusic)
+importFrom(MuSiC,music_prop)
+importFrom(MuSiC,music_prop.cluster)
+importFrom(S4Vectors,DataFrame)
+importFrom(S4Vectors,metadata)
+importFrom(SummarizedExperiment,colData)
+importFrom(dplyr,left_join)
 importFrom(magrittr,"%>%")
+importFrom(stats,dist)
+importFrom(stats,hclust)
+importFrom(tibble,column_to_rownames)
+importFrom(tibble,rownames_to_column)
+importFrom(tidyr,gather)

R/data.R

@@ -0,0 +1,22 @@
+#' @name musicBulkexample
+#' @title example bulk data for this package
+#' @docType data
+#' @format matrix
+#' @source Processed RNA-seq data from bulk kidney in healthy and APOL1 mouse (Beckerman et al.)
+#' @keywords datasets
+#' @usage data("musicBulkexample")
+#' @examples
+#' data("mouseBrainSubsetSCE")
+"musicBulkexample"
+
+
+#' @name musicSCEexample
+#' @title example single cell data for this package
+#' @docType data
+#' @format SingleCellExperiment
+#' @source Subset of single cell RNA-seq data of mouse kidney (Park et al.)
+#' @keywords datasets
+#' @usage data("musicSCEexample")
+#' @examples
+#' data("musicSCEexample")
+"musicSCEexample"

R/descriptions.R

@@ -1,4 +1,8 @@
 #' @export
+#' @description prints music desc
+#' @name description_runMusic
+#' @title prints description of music wrapper parameters 
+
 
 description_runMusic <- function() {
   return(list(
@@ -11,7 +15,7 @@ description_runMusic <- function() {
     samples = "default is sampleID character,the colData of single cell dataset used as samples", 
     preClusterlist = "pre grouped cluster list" ,
     DEmarkers = "list of group marker",
-    groups = "roups passes the column name of higher-cluster in phenoData", 
+    groups = "groups passes the column name of higher-cluster in phenoData", 
     selectCt = "vector of cell types, default as NULL. If NULL, then use all cell types provided by single cell dataset", #same as select.ct
     cellSize = "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", #same as cell_size 
     ctCov = "logical. If TRUE, use the covariance across cell types", #same as ctCov

R/plotMusicResults.R

@@ -1,3 +1,5 @@
+#' plotMusicResults function
+#'
 #' @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.
@@ -6,18 +8,18 @@
 #' @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
+#' @param colDataName The column name(s) in \code{colData} that need
+#' to be added to the annotation. See plotSCEHeatmap from SingleCellTK for more info
+#' @param rowDataName The column name(s) in \code{rowData} that need
+#' to be added to the annotation
+#' @param useAssay Choose the assay to be plotted with the heatmap. 
+#' @param scale scale input assay if set to TRUE. Default is FALSE
 #' @return SingleCellExperiment object containing the outputs of the
 #'  specified algorithms in the \link{colData}
 #' of \code{inSCE}.
 #' 
 #' @export
 
-require(singleCellTK)
-require(ggplot2)
-require(dplyr)
-require(S4Vectors)
-require(SingleCellExperiment)
-
 
 plotMusicResults<- function(inSCE, 
                             analysisType = c("EstCellProp","PreGroupedClustProp","SingleCellClust"),
@@ -57,18 +59,24 @@ plotMusicResults<- function(inSCE,
 
 
 
-
+    col_fun<-colorRamp2(c(0,0.2,0.4,0.6,0.8,1), hcl_palette = "RdBu")
     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,
-                            scale = scale)
+    heatmap<-singleCellTK::plotSCEHeatmap(bulkinSCE,  # Check version
+                                          useAssay = useAssay, 
+                                          rowLabel = T, 
+                                          colLabel = T, 
+                                          rowTitle = "Subjects",
+                                          colTitle = "CellType",
+                                          rowLabelSize = 10, 
+                                          colLabelSize = 10,
+                                          colorScheme = col_fun,
+                                          colDataName = colDataName,
+                                          rowDataName = rowDataName,
+                                          trim = c(0,1),
+                                          title = heatmapTitle,
+                                          scale = scale)
     return(heatmap)
   }
 
@@ -78,25 +86,25 @@ plotMusicResults<- function(inSCE,
 
   if(analysisType == "SingleCellClust"){
     plots<-.musicPlotclusters(inSCE,analysisName = analysisName)
-  #  metadata(inSCE)$sctk$music[[analysisName]][["Clusters"]]<- temp_results 
+    #  metadata(inSCE)$sctk$music[[analysisName]][["Clusters"]]<- temp_results 
   }
   else if(analysisType == "EstCellProp"){
 
-    plots<-.plotHeatmap(inSCE,heatmapTitle = heatmapTitle,useAssay = "Est.prop.weighted" ,analysisName = analysisName )
+    plots<-.plotHeatmap(inSCE,heatmapTitle = heatmapTitle,useAssay = "Est.prop.weighted" ,analysisName = analysisName, colDataName = colDataName, rowDataName = rowDataName,scale = scale )
     # 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 )
+
+    plots<- .plotHeatmap(inSCE,heatmapTitle = heatmapTitle,useAssay = "Est.prop.weighted.cluster",analysisName = analysisName, colDataName = colDataName, rowDataName = rowDataName,scale = scale  )
     #metadata(inSCE)$sctk$music[[analysisName]][["Heatmap"]]<- temp_results 
 
   }
-
-
+  
+  
   return(plots)
 } 
 

R/reportMusic.R

@@ -1,6 +1,5 @@
 
 # Report render functions for music
-
 #' @title Deconvolution of RNASeq data using single cell data
 #' @description A wrapper that performs deconvolution and clustering using MuSiC tool and 
 #' SingleCellExperiment object
@@ -19,19 +18,26 @@
 #' @param ctCov logical. If TRUE, use the covariance across cell types; #same as ctCov in MuSiC
 #' @param preClusterlist 	list of cell types. The list identify groups of similar cell types.
 #' @param verbose logical, default as TRUE.
-#' @param iter.max 	numeric, maximum iteration number. Default 1000
+#' @param iterMax 	numeric, maximum iteration number, same as iter.max in MuSiC. Default 1000
 #' @param nu  regulation parameter, take care of weight when taking reciprocal 1e-04,
 #' @param eps Threshold of convergence. Default 0.01,
 #' @param centered logic, subtract avg of Y and D. Default FALSE
 #' @param normalize logic, divide Y and D by their standard deviation. Default FALSE
+#' @param bulkData matrix of bulk RNASeq data
+#' @param nonZero logical, default as TRUE. If true, remove all gene with zero expression, same as non.zero.
+#' @param groups grouping labels, character, the colData of single cell data used as groups
+#' @param output_file name of the output file 
+#' @param DEmarkers list of gene names. The list include differential expressed genes within groups. List name must be the same as group.markers.
+#' @param output_dir name of output marker
 #' @return SingleCellExperiment object containing the outputs of the specified algorithms in the \link{colData} of \code{inSCE}.
+#' @export reportMusicAll
 #' @export
 #' @examples
-#' data(scExample, package = "singleCellTK")
-#' Add bulk data here
 #' \dontrun{
-#' reportMusic(inSCE = Mouse.sce, 
-#' bulkData = mouse_bulk,
+#' data("musicSCEexample")
+#' data("musicBulkexample")
+#' music_sce <- reportMusicAll(inSCE = musicSCEexample, 
+#' bulkData = musicBulkexample,
 #' analysisName = "test1",
 #' analysisType = "EstCellProp", 
 #' markers = NULL, 
@@ -53,11 +59,10 @@
 #' output_file = ,
 # ' output_dir = NULL)
 #' }
-
 #' \dontrun{
-#' reportMusicResults(inSCE= new_sce_with_music_basis2,
+#' reportMusicAll(inSCE= music_sce,
 #'                   analysisName = "test2",
-#'                   analysisType = "SingleCellClust", 
+#'                   analysisType = "EstCellProp", 
 #'                   heatmapTitle = "test")
 
 
@@ -121,7 +126,8 @@ reportMusic <- function(inSCE = inSCE,
 
 }
 
-
+#' reportMusicResults
+#' @export
 
 reportMusicResults<- function(inSCE,
                               analysisName,
@@ -146,6 +152,9 @@ reportMusicResults<- function(inSCE,
 
 }
 
+#' reportMusicAll
+#' @export
+
 
 reportMusicAll<-function(inSCE = inSCE, 
                          bulkData = bulkData,