diff --git a/.Rbuildignore b/.Rbuildignore old mode 100644 new mode 100755 diff --git a/.github/.gitignore b/.github/.gitignore old mode 100644 new mode 100755 diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml old mode 100644 new mode 100755 diff --git a/.gitignore b/.gitignore old mode 100644 new mode 100755 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml old mode 100644 new mode 100755 diff --git a/DESCRIPTION b/DESCRIPTION old mode 100644 new mode 100755 diff --git a/DeconvExplorer.Rproj b/DeconvExplorer.Rproj old mode 100644 new mode 100755 diff --git a/LICENSE b/LICENSE old mode 100644 new mode 100755 diff --git a/LICENSE.md b/LICENSE.md old mode 100644 new mode 100755 diff --git a/NAMESPACE b/NAMESPACE old mode 100644 new mode 100755 diff --git a/NEWS.md b/NEWS.md old mode 100644 new mode 100755 diff --git a/R/BenchmarkingPlots.R b/R/BenchmarkingPlots.R old mode 100644 new mode 100755 diff --git a/R/DeconvExplorer-pkg.R b/R/DeconvExplorer-pkg.R old mode 100644 new mode 100755 diff --git a/R/DeconvExplorer.R b/R/DeconvExplorer.R old mode 100644 new mode 100755 index 8187b62..9ee0f91 --- a/R/DeconvExplorer.R +++ b/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", @@ -511,7 +513,7 @@ 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) @@ -519,27 +521,29 @@ DeconvExplorer <- function(deconvexp_bulk = 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" + ) ) ) ), @@ -547,7 +551,7 @@ DeconvExplorer <- function(deconvexp_bulk = NULL, 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", diff --git a/R/Global.R b/R/Global.R old mode 100644 new mode 100755 diff --git a/R/SignatureExplorationPlots.R b/R/SignatureExplorationPlots.R old mode 100644 new mode 100755 index 4091970..519edf4 --- a/R/SignatureExplorationPlots.R +++ b/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)) } diff --git a/R/SignatureRefinements.R b/R/SignatureRefinements.R old mode 100644 new mode 100755 index f5a630b..ba61bc9 --- a/R/SignatureRefinements.R +++ b/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, ] diff --git a/R/zzz.R b/R/zzz.R old mode 100644 new mode 100755 diff --git a/README.md b/README.md old mode 100644 new mode 100755 diff --git a/inst/deconvexplorer-webserver/app/CIBERSORT.R b/inst/deconvexplorer-webserver/app/CIBERSORT.R old mode 100644 new mode 100755 diff --git a/inst/deconvexplorer-webserver/app/Dockerfile b/inst/deconvexplorer-webserver/app/Dockerfile old mode 100644 new mode 100755 index f9cab20..0310197 --- a/inst/deconvexplorer-webserver/app/Dockerfile +++ b/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 diff --git a/inst/deconvexplorer-webserver/app/app.R b/inst/deconvexplorer-webserver/app/app.R old mode 100644 new mode 100755 diff --git a/inst/deconvexplorer-webserver/app/shiny-server.conf b/inst/deconvexplorer-webserver/app/shiny-server.conf old mode 100644 new mode 100755 diff --git a/inst/deconvexplorer-webserver/app/shiny-server.sh b/inst/deconvexplorer-webserver/app/shiny-server.sh old mode 100644 new mode 100755 diff --git a/inst/deconvexplorer-webserver/docker-compose.yml b/inst/deconvexplorer-webserver/docker-compose.yml old mode 100644 new mode 100755 diff --git a/inst/deconvexplorer-webserver/nginx/nginx.conf b/inst/deconvexplorer-webserver/nginx/nginx.conf old mode 100644 new mode 100755 diff --git a/inst/deconvexplorer-webserver/shinyproxy/Dockerfile b/inst/deconvexplorer-webserver/shinyproxy/Dockerfile old mode 100644 new mode 100755 diff --git a/inst/deconvexplorer-webserver/shinyproxy/application.yml b/inst/deconvexplorer-webserver/shinyproxy/application.yml old mode 100644 new mode 100755 diff --git a/inst/extdata/app_information.Rmd b/inst/extdata/app_information.Rmd old mode 100644 new mode 100755 diff --git a/inst/extdata/app_information.md b/inst/extdata/app_information.md old mode 100644 new mode 100755 diff --git a/inst/extdata/data_info.md b/inst/extdata/data_info.md old mode 100644 new mode 100755 diff --git a/inst/extdata/deconvolution_example.rds b/inst/extdata/deconvolution_example.rds old mode 100644 new mode 100755 diff --git a/inst/extdata/signature_example.rds b/inst/extdata/signature_example.rds old mode 100644 new mode 100755 diff --git a/inst/extdata/tour_intro.txt b/inst/extdata/tour_intro.txt old mode 100644 new mode 100755 diff --git a/inst/www/batch.png b/inst/www/batch.png old mode 100644 new mode 100755 diff --git a/inst/www/bulk.png b/inst/www/bulk.png old mode 100644 new mode 100755 diff --git a/inst/www/cell_anno.png b/inst/www/cell_anno.png old mode 100644 new mode 100755 diff --git a/inst/www/deconv.png b/inst/www/deconv.png old mode 100644 new mode 100755 diff --git a/inst/www/deconvExplorer.png b/inst/www/deconvExplorer.png deleted file mode 100644 index 3697237..0000000 Binary files a/inst/www/deconvExplorer.png and /dev/null differ diff --git a/inst/www/markers.png b/inst/www/markers.png old mode 100644 new mode 100755 diff --git a/inst/www/omnideconv_logo.svg b/inst/www/omnideconv_logo.svg deleted file mode 100644 index 0de7b56..0000000 --- a/inst/www/omnideconv_logo.svg +++ /dev/null @@ -1,349 +0,0 @@ - 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