App finalize

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

@@ -18,11 +18,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: macOS-latest, r: "release" }
-          - { os: windows-latest, r: "release" }
           - { os: ubuntu-latest, r: "devel", http-user-agent: "release" }
           - { os: ubuntu-latest, r: "release" }
-          - { os: ubuntu-latest, r: "oldrel-1" }
+          #- { os: ubuntu-latest, r: "oldrel-1" }
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

DESCRIPTION

@@ -23,6 +23,7 @@ Depends:
 Imports: 
     shiny,
     shinydashboard,
+    shinyBS,
     omnideconv, 
     plotly,
     ggplot2, 
@@ -49,7 +50,7 @@ Imports:
     stats,
     circlize,
     BioQC
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Encoding: UTF-8
 Remotes: 
     github::omnideconv/omnideconv
@@ -59,5 +60,10 @@ Suggests:
     bookdown,
     testthat (>= 3.0.0), 
     markdown
+biocViews:
+    Software, GeneExpression, ImmunoOncology, Sequencing, Transcription, 
+    Classification, Transcriptomics, Visualization
+URL: https://github.com/omnideconv/DeconvExplorer/
+BugReports: https://github.com/omnideconv/DeconvExplorer/issues
 VignetteBuilder: knitr
 Config/testthat/edition: 3

NAMESPACE

@@ -2,6 +2,7 @@
 
 export(DeconvExplorer)
 export(download_signatureUpset)
+export(errorModal)
 export(plot_benchmark_correlation)
 export(plot_benchmark_rmse)
 export(plot_benchmark_scatter)
@@ -14,10 +15,10 @@ export(removePercentZeros)
 export(removeUnspecificGenes)
 export(renameCellType)
 export(returnSelectedDeconvolutions)
-export(scoreEntropy)
 export(selectGenesByScore)
 import(omnideconv)
 import(shiny, except = c(renderDataTable, dataTableOutput))
+import(shinyBS)
 importFrom(ComplexHeatmap,Heatmap)
 importFrom(ComplexHeatmap,UpSet)
 importFrom(ComplexHeatmap,comb_size)
@@ -50,6 +51,7 @@ importFrom(ggplot2,geom_col)
 importFrom(ggplot2,geom_hline)
 importFrom(ggplot2,geom_jitter)
 importFrom(ggplot2,geom_point)
+importFrom(ggplot2,geom_rect)
 importFrom(ggplot2,geom_text)
 importFrom(ggplot2,geom_tile)
 importFrom(ggplot2,ggplot)

R/BenchmarkingPlots.R

@@ -47,24 +47,20 @@ plot_benchmark_scatter <- function(gtruth_df,
 
   # merge
   merged.df <- merge(df, ref, all.x = TRUE) # keep all deconvolution results
+  merged.df <- merged.df[complete.cases(merged.df), ]
 
   # build plot
   plot <- ggplot(merged.df, aes(x = .data$truth, y = .data$estimate, color = .data$cell_type)) +
-    geom_point(show.legend = FALSE) +
-    ggpubr::stat_cor(label.sep = "\n", size = 3, color = "black", label.x.npc = 0.01) +
+    geom_point(show.legend = FALSE, size = 3, alpha = .8) +
+    ggpubr::stat_cor(label.sep = "\n", size = 3, color = "black", label.x.npc = 0.05, label.y = max(merged.df$estimate) + 0.05, vjust = 1) +
     ggforce::facet_grid_paginate(method ~ .data$cell_type,
-      margins = c("cell_type"), scales = "free"
+      margins = c("cell_type")
     ) +
     ggplot2::theme_bw() +
-    theme(axis.text.x = element_text(angle = 60, hjust = 1)) +
+    theme(axis.text.x = element_text(angle = 60, hjust = 1), strip.background = element_rect(fill = "white")) +
     labs(x = "true cellular fractions", y = "cell type estimates", title = "") +
-    theme(legend.position = "none", text = element_text(size = 15))
-
-  plot <- plot + geom_abline() +
-    ggforce::facet_grid_paginate(method ~ .data$cell_type,
-      margins = c("cell_type"), scales = "free"
-    ) +
-    theme(axis.text.x = element_text(angle = 60, hjust = 1))
+    theme(legend.position = "none", text = element_text(size = 15)) +
+    geom_abline(linetype = "dashed")
 
   # get palette
   max_colors <- RColorBrewer::brewer.pal.info[color_palette, ]$maxcolors # for brewer.pal()

R/DeconvExplorer-pkg.R

@@ -11,7 +11,7 @@
 #' @importFrom ggplot2 aes aes_ aes_string coord_cartesian coord_flip element_text
 #' facet_wrap geom_abline geom_boxplot geom_col geom_jitter geom_point
 #' geom_tile ggplot guide_colorbar guides labs scale_fill_gradient theme geom_text element_blank
-#' geom_hline scale_colour_brewer scale_fill_brewer ylim theme_minimal
+#' geom_hline scale_colour_brewer scale_fill_brewer ylim theme_minimal geom_rect
 #' @importFrom shinycssloaders withSpinner
 #' @importFrom waiter Waitress
 #' @importFrom rlang .data
@@ -32,7 +32,8 @@
 #' @importFrom ggpubr stat_cor
 #' @importFrom corrplot corrplot
 #' @importFrom SummarizedExperiment assays
+#' @import shinyBS
 #'
 #' @name DeconvExplorer-pkg
 #' @docType package
-NULL
+"_PACKAGE"