Merge pull request #68 from omnideconv/alex_dev

Make DeconvExplorer ready for the GCB

DESCRIPTION

@@ -32,32 +32,33 @@ Imports:
     shiny,
     shinydashboard,
     shinyBS,
-    omnideconv, 
+    omnideconv,
     plotly,
-    ggplot2, 
+    ggplot2,
     ggpubr,
     corrplot,
     ggforce,
     SummarizedExperiment,
-    shinycssloaders, 
+    shinycssloaders,
     waiter,
-    rintrojs, 
-    DT, 
-    shinyjs, 
-    stringr, 
-    tidyr, 
+    rintrojs,
+    DT,
+    shinyjs,
+    stringr,
+    tidyr,
     rlang,
     utils,
-    tools, 
+    tools,
     vroom,
     ComplexHeatmap,
     grid,
-    InteractiveComplexHeatmap, 
+    InteractiveComplexHeatmap,
     RColorBrewer,
     grDevices,
     stats,
     circlize,
-    BioQC
+    BioQC,
+    shinyWidgets
 RoxygenNote: 7.3.1
 Encoding: UTF-8
 Remotes: 

NAMESPACE

@@ -85,6 +85,7 @@ importFrom(rintrojs,introjsUI)
 importFrom(rintrojs,readCallback)
 importFrom(rlang,.data)
 importFrom(shiny,addResourcePath)
+importFrom(shinyWidgets,actionBttn)
 importFrom(shinyBS,bsPopover)
 importFrom(shinycssloaders,withSpinner)
 importFrom(shinydashboard,box)

R/BenchmarkingPlots.R

@@ -57,10 +57,10 @@ plot_benchmark_scatter <- function(gtruth_df,
       margins = c("cell_type")
     ) +
     ggplot2::theme_bw() +
-    theme(axis.text.x = element_text(angle = 60, hjust = 1), strip.background = element_rect(fill = "white")) +
+    theme(axis.text.x = element_text(angle = 60, hjust = 1), strip.background = ggplot2::element_rect(fill = "white")) +
     labs(x = "true cellular fractions", y = "cell type estimates", title = "") +
     theme(legend.position = "none", text = element_text(size = 15)) +
-    geom_abline(linetype = "dashed")
+    ggplot::geom_abline(linetype = "dashed")
 
   # get palette
   max_colors <- RColorBrewer::brewer.pal.info[color_palette, ]$maxcolors # for brewer.pal()

R/DeconvExplorer-pkg.R

@@ -8,11 +8,10 @@
 #' dashboardSidebar dropdownMenu menuItem notificationItem sidebarMenu valueBox valueBoxOutput renderValueBox
 #' tabItem tabItems
 #' @importFrom plotly ggplotly plotlyOutput renderPlotly plot_ly layout config
-#' @importFrom ggplot2 aes aes_ aes_string coord_cartesian coord_flip
-#' element_rect 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 ggsave
-#' scale_colour_brewer scale_fill_brewer ylim theme_minimal geom_rect
+#' @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_rect element_rect
 #' @importFrom shinycssloaders withSpinner
 #' @importFrom waiter Waitress waiter_hide waiter_show waiter_show_on_load
 #' waiter_update
@@ -37,8 +36,8 @@
 #' @importFrom ggpubr stat_cor
 #' @importFrom corrplot corrplot
 #' @importFrom SummarizedExperiment assays
-#' @importFrom BioQC entropySpecificity gini
-#' @importFrom shinyBS bsPopover
+#' @importFrom shinyWidgets actionBttn
+#' @import shinyBS
 #'
 #' @name DeconvExplorer-pkg
 #' @docType package