Alex dev

R/DeconvExplorer.R

@@ -201,7 +201,7 @@ DeconvExplorer <- function(deconvexp_bulk = NULL,
     column(
       width = 4,
       selectInput("deconvMethod", "Deconvolution Method",
-        choices = c('MuSiC'='music', omnideconv::deconvolution_methods[-10])
+        choices = c("MuSiC" = "music", omnideconv::deconvolution_methods[-10])
       )
     ),
     column(
@@ -220,8 +220,10 @@ DeconvExplorer <- function(deconvexp_bulk = NULL,
     column(
       width = 3,
       div(
-        shinyBS::popify(shinyWidgets::actionBttn("deconvolute", "Deconvolute", style = 'simple', icon = icon('triangle-exclamation'), color = 'warning'),
-                        "Attention", "Some methods are considerably slower than others; please keep this in mind when using DeconvExplorer for deconvolution."),
+        shinyBS::popify(
+          shinyWidgets::actionBttn("deconvolute", "Deconvolute", style = "simple", icon = icon("triangle-exclamation"), color = "warning"),
+          "Attention", "Some methods are considerably slower than others; please keep this in mind when using DeconvExplorer for deconvolution."
+        ),
         style = "margin-top:1.7em"
       )
     ),
@@ -234,7 +236,7 @@ DeconvExplorer <- function(deconvexp_bulk = NULL,
       title = "",
       content = "Select a deconvolution method to run. If required and supported by the deconvolution method you can additionally select a custom signature to be used in computation. Please note this is an advanced feature and should be used with caution. "
     )
-  
+
 
   deconv_plot_box <- shinydashboard::box(
     id = "tour_deconvPlot",
@@ -511,43 +513,45 @@ DeconvExplorer <- function(deconvexp_bulk = NULL,
     title = span("Clustered Signature", icon("question-circle", id = "sigHeatmapQ")),
     status = "info", solidHeader = TRUE,
     width = 12,
-    fluidRow(    
+    fluidRow(
       column(
         width = 4,
         selectInput("signatureToHeatmap", "Select a Signature", choices = NULL)
       ),
       column(
         width = 2,
         selectInput("signatureAnnotationScore", "Select an annotation score",
-                    choices = c("Entropy" = "entropy", "Gini Index" = "gini")
+          choices = c("Entropy" = "entropy", "Gini Index" = "gini")
         )
       ),
       column(
         width = 2,
         selectInput("signatureAnnotationPlotType", "Annotation Type",
-                    choices = c("Bars" = "bar", "Lines" = "line")
+          choices = c("Bars" = "bar", "Lines" = "line")
         )
       ),
       column(
         width = 2,
         selectInput("clusterCelltypes", "Order rows (cell types)",
-                    choices = c(".. by cell-type similarity" = "cluster", ".. alphabetically" = "no_cluster")
+          choices = c(".. by cell-type similarity" = "cluster", ".. alphabetically" = "no_cluster")
         )
       ),
       column(
         width = 2,
         selectInput("clusterGenes", "Order columns (genes)",
-                    choices = c(".. by maximal z-score per cell type" = "z-score cutoff",
-                                ".. hierarchically based on euclidean distance" = "hierarchical clustering",
-                                ".. alphabetically" = "alphabetical")
+          choices = c(
+            ".. by maximal z-score per cell type" = "z-score cutoff",
+            ".. hierarchically based on euclidean distance" = "hierarchical clustering",
+            ".. alphabetically" = "alphabetical"
+          )
         )
       )
     ),
     fluidRow(
       column(
         width = 12,
         InteractiveComplexHeatmap::originalHeatmapOutput("clusteredHeatmapOneSignature",
-                                                         width = "1250px", height = "450px", containment = TRUE
+          width = "1250px", height = "450px", containment = TRUE
         )
       )
     ),
@@ -725,7 +729,7 @@ DeconvExplorer <- function(deconvexp_bulk = NULL,
       column(
         width = 7,
         sliderInput("refinePercentZero", "Maximum percentage of zeroes allowed for each gene",
-                    min = 0, max = 100, value = 90, step = 1, post = "%"
+          min = 0, max = 100, value = 90, step = 1, post = "%"
         )
       ),
       column(
@@ -759,7 +763,7 @@ DeconvExplorer <- function(deconvexp_bulk = NULL,
     )
   )
 
-refUnspecificPopover <-
+  refUnspecificPopover <-
     shinyBS::bsPopover(
       id = "refUnspecificQ",
       title = "",
@@ -817,8 +821,8 @@ refUnspecificPopover <-
     shinyBS::bsPopover(
       id = "refManuallyQ",
       title = "",
-      content = 
-    )
+      content =
+      )
 
   # Info Boxes --------------------------------------------------------------
   info_overview <- shinydashboard::box(
@@ -1661,7 +1665,7 @@ refUnspecificPopover <-
           scoring_method = input$signatureAnnotationScore,
           annotation_type = input$signatureAnnotationPlotType,
           color_palette = input$globalColor,
-          order_rows = input$clusterCelltypes, 
+          order_rows = input$clusterCelltypes,
           order_columns = input$clusterGenes
         ),
         "clusteredHeatmapOneSignature",

R/SignatureExplorationPlots.R

@@ -253,22 +253,19 @@ plot_signatureClustered <- function(signature_mat,
     cell.types.ordered <- order(colnames(mat))
   }
 
-  if(order_columns == 'z-score cutoff'){
+  if (order_columns == "z-score cutoff") {
     genes <- c()
     for (c in cell.types.ordered) {
       highly.expr.genes <- names(which(mat[, c] > threshold))
       genes <- union(genes, highly.expr.genes)
     }
-    
+
     genes <- union(genes, rownames(mat))
-  }else if(order_columns == 'hierarchical clustering'){
-
+  } else if (order_columns == "hierarchical clustering") {
     # use hierarchical ward D2 clustering based on euclidean distance
-    clustering <- hclust(dist(mat), method = 'ward.D2')
+    clustering <- hclust(dist(mat), method = "ward.D2")
     genes <- rownames(mat)[clustering$order]
-
-  }else if(order_columns == 'alphabetical'){
-
+  } else if (order_columns == "alphabetical") {
     genes <- sort(rownames(mat))
   }
 

R/SignatureRefinements.R

@@ -116,26 +116,26 @@ removeUnspecificGenes <- function(signature_mat,
 
   signature_mat <- as.matrix(signature_mat)
 
-  to_keep <- sapply(1:nrow(signature_mat), function(i){
+  to_keep <- sapply(1:nrow(signature_mat), function(i) {
     row <- signature_mat[i, ] # has colnames! drop FALSE is mandatory !!!!!
-    
+
     # calculate bins to prevent error
     breaks <- seq(floor(min(row)), ceiling(max(row)), length.out = number_of_bins + 1)
-    
+
     # cut into bins, seperate for each gene
     bins <- cut(row, breaks = breaks, labels = labels, include.lowest = TRUE)
-    
+
     nHighBins <- sum(bins == "high") # not working when labels is something else
-    
+
     # this value needs to be greater than one, depending of the step in the pipeline there arent
     # any rows producing zeros left but that is not the case for all signatures
     if (nHighBins <= max_count & nHighBins > 0) {
       return(TRUE)
-    }else{
+    } else {
       return(FALSE)
     }
   })
-  
+
 
   refinedSignature <- signature_mat[to_keep, ]
 

inst/deconvexplorer-webserver/app/Dockerfile

@@ -27,9 +27,11 @@ RUN apt-get update && apt-get install -y \
 # omnideconv and DeconvExplorer
 #RUN install2.r --error textshaping
 
-RUN R -e "install.packages('pak')"
+RUN R -e "install.packages(c('pak','devtools'))"
 RUN R -e "pak::pkg_install(c('car', 'matlib', 'remotes'))"
-RUN R -e "remotes::install_github('omnideconv/omnideconv', dependencies=TRUE)"
+RUN R -e "remotes::install_github('renozao/NMF@devel', auth_token='TOKEN')"
+RUN R -e "remotes::install_github('omnideconv/BayesPrism', auth_token='TOKEN')"
+RUN R -e "remotes::install_github('omnideconv/omnideconv', dependencies=TRUE, auth_token='TOKEN')"
 RUN R -e "pak::pkg_install('omnideconv/DeconvExplorer', dependencies=TRUE)"
 
 #RUN R -e "reticulate::install_miniconda()" # will not install automatically