Merge pull request #2 from jiajic/main

GiottoVisuals semi-functional
drieslab · Aug 28, 2023 · 328d973 · 328d973
2 parents 207c789 + c513ddd
commit 328d973
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -3,3 +3,4 @@
 ^LICENSE\.md$
 ^README\.Rmd$
 ^.github$
+^codecov.yml$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: GiottoVisuals
 Title: What the Package Does (One Line, Title Case)
-Version: 0.0.0.9001
+Version: 0.0.0.9002
 Authors@R: c(
 	person("Ruben", "Dries", email = "[email protected]",
 		 role = c("aut", "cre")),
@@ -28,17 +28,21 @@ Depends:
     GiottoUtils,
     GiottoClass
 Imports:
+    checkmate,
+    colorRamp2,
     cowplot (>= 0.9.4),
     data.table,
     ggplot2 (>= 3.1.1),
     ggrepel,
-    graphics,
+    igraph (>= 1.2.4.1),
     methods,
     plotly,
     RColorBrewer (>= 1.1-2),
+    reshape2,
     scales (>= 1.0.0),
     scattermore,
-    stats
+    stats,
+    terra
 Suggests:
     ComplexHeatmap (>= 1.20.0),
     ggalluvial,
@@ -47,41 +51,45 @@ Suggests:
     ggraph,
     ggsci,
     GiottoData,
-    networkd3,
+    htmlwidgets,
+    Matrix,
+    networkD3,
     NineteenEightyR,
     nord,
     palr,
     palettetown,
+    png,
     rcartocolor,
-    shiny,
+    remotes,
+    scatterpie,
+    tiff,
     viridis,
     viridisLite,
     wesanderson,
-    testthat (>= 3.0.0),
+    testthat (>= 3.0.0)
 Remotes:
     drieslab/GiottoUtils,
     drieslab/GiottoClass
 Config/testthat/edition: 3
 Collate: 
-    'aux_dendrogram.R'
-    'aux_heatmap.R'
-    'aux_scatterplot.R'
-    'aux_violinplot.R'
-    'plot_save.R'
-    'auxilliary_visuals.R'
+    'aux_defaults.R'
+    'aux_output.R'
+    'aux_save.R'
+    'aux_visuals.R'
     'color_palettes.R'
     'dd.R'
-    'defaults.R'
     'gg_info_layers.R'
     'globals.R'
-    'hvf_plots.R'
-    'image_visuals.R'
-    'interactivity.R'
     'package_imports.R'
-    'pc_plots.R'
-    'plot_output.R'
-    'spatial_DE_visuals.R'
-    'spatial_in_situ_visuals.R'
-    'spatial_interaction_visuals.R'
-    'spatial_visuals.R'
+    'plot_dendrogram.R'
+    'plot_heatmap.R'
+    'plot_scatter.R'
+    'plot_violin.R'
+    'spatialDE_visuals.R'
+    'vis_hvf.R'
+    'vis_pc.R'
+    'vis_spatial.R'
+    'vis_spatial_in_situ.R'
+    'vis_spatial_interaction.R'
+    'viz_spatial_network.R'
     'zzz.R'
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,20 +1,19 @@
 # Generated by roxygen2: do not edit by hand
 
 export(FSV_show)
-export(addPolygonCells)
 export(cellProximityBarplot)
 export(cellProximityHeatmap)
 export(cellProximityNetwork)
 export(cellProximitySpatPlot)
 export(cellProximitySpatPlot2D)
 export(cellProximitySpatPlot3D)
 export(cellProximityVisPlot)
-export(compareCellAbundance)
-export(comparePolygonExpression)
 export(create_calc_var_HVF_plot)
+export(create_cluster_dendrogram)
 export(create_cov_group_HVF_plot)
 export(create_cov_loess_HVF_plot)
 export(create_jackstrawplot)
+export(create_screeplot)
 export(dimCellPlot)
 export(dimCellPlot2D)
 export(dimFeatPlot2D)
@@ -23,45 +22,35 @@ export(dimPlot)
 export(dimPlot2D)
 export(dimPlot3D)
 export(expand_feature_info)
-export(getCellsFromPolygon)
 export(getColors)
 export(getDistinctColors)
 export(gg_simple_scatter)
 export(plotCCcomDotplot)
 export(plotCCcomHeatmap)
 export(plotCPF)
-export(plotCPG)
 export(plotCellProximityFeats)
-export(plotCellProximityGenes)
 export(plotCombineCCcom)
-export(plotCombineCPG)
 export(plotCombineCellCellCommunication)
-export(plotCombineCellProximityGenes)
 export(plotCombineICF)
 export(plotCombineInteractionChangedFeats)
-export(plotCombineInteractionChangedGenes)
 export(plotHeatmap)
 export(plotICF)
-export(plotICG)
 export(plotInteractionChangedFeats)
-export(plotInteractionChangedGenes)
-export(plotInteractivePolygons)
 export(plotMetaDataCellsHeatmap)
 export(plotMetaDataHeatmap)
 export(plotPCA)
 export(plotPCA_2D)
 export(plotPCA_3D)
-export(plotPolygons)
 export(plotRankSpatvsExpr)
 export(plotRecovery)
+export(plotStatDelaunayNetwork)
 export(plotTSNE)
 export(plotTSNE_2D)
 export(plotTSNE_3D)
 export(plotUMAP)
 export(plotUMAP_2D)
 export(plotUMAP_3D)
 export(plot_output_handler)
-export(select_gimage)
 export(showClusterDendrogram)
 export(showClusterHeatmap)
 export(showColorInstructions)
@@ -82,6 +71,9 @@ export(spatGenePlot3D)
 export(spatInSituPlotDensity)
 export(spatInSituPlotHex)
 export(spatInSituPlotPoints)
+export(spatNetwDistributions)
+export(spatNetwDistributionsDistance)
+export(spatNetwDistributionsKneighbors)
 export(spatPlot)
 export(spatPlot2D)
 export(spatPlot3D)
@@ -91,6 +83,8 @@ import(GiottoUtils)
 import(ggplot2)
 import(utils)
 importClassesFrom(data.table,data.table)
+importFrom(data.table,dcast)
+importFrom(data.table,dcast.data.table)
 importFrom(methods,slot)
 importFrom(stats,cov)
 importFrom(stats,var)
diff --git a/R/defaults.R → R/aux_defaults.R b/R/defaults.R → R/aux_defaults.R
@@ -196,18 +196,18 @@ set_default_color_continuous <- function(
   # select gradient functions to use
   grad <- switch(
     type,
-    'fill' = ggplot2::scale_fill_gradient(),
-    'color' = ggplot2::scale_color_gradient()
+    'fill' = ggplot2::scale_fill_gradient,
+    'color' = ggplot2::scale_color_gradient
   )
   gradn <- switch(
     type,
-    'fill' = ggplot2::scale_fill_gradientn(),
-    'color' = ggplot2::scale_color_gradientn()
+    'fill' = ggplot2::scale_fill_gradientn,
+    'color' = ggplot2::scale_color_gradientn
   )
   grad2 <- switch(
     type,
-    'fill' = ggplot2::scale_fill_gradient2(),
-    'color' = ggplot2::scale_color_gradient2()
+    'fill' = ggplot2::scale_fill_gradient2,
+    'color' = ggplot2::scale_color_gradient2
   )
 
   # global giotto options
@@ -243,6 +243,8 @@ set_default_color_continuous <- function(
                                                     ...),
     'sequential' = evaluate_color_gradient_sequential(colors = colors,
                                                       reverse = reverse,
+                                                      gradn = gradn,
+                                                      grad = grad,
                                                       ...)
   )
 }
@@ -461,6 +463,9 @@ set_default_color_continuous_CCcom_dotplot = function(
 #' @export
 showColorInstructions <- function() {
 
+  # DT vars
+  option = default = description = NULL
+
   out = giotto_color_instructions[, paste(
     '\noption      : ', color_blue(option),
     '\ndefault     : ', default,

diff --git a/R/plot_output.R → R/aux_output.R b/R/plot_output.R → R/aux_output.R
@@ -18,7 +18,7 @@
 #' the plot in display device
 #' @param default_save_name default name to use (should be set by the specific
 #' plotting function. Users should not interact with this parameter)
-#' @param save_param list of plot saving parameters see [showSaveParameters]
+#' @param save_param list of plot saving parameters see [showSaveParameters()]
 #' @param else_return optional. What should be returned instead if the plot
 #' object is not returned
 #' @keywords internal
@@ -62,13 +62,63 @@ plot_output_handler = function(gobject,
 
   ## return plot ##
   if(return_plot) {
-    invisible(return(plot_object))
+    return(invisible(plot_object))
   } else {
-    return(else_return)
+    return(invisible(else_return))
   }
 }
 
 
+# TODO split into two functions
+#' plot_output_handler_read = function(gobject,
+#'                                 plot_object,
+#'                                 save_plot = NA,
+#'                                 return_plot = NA,
+#'                                 show_plot = NA,
+#'                                 default_save_name,
+#'                                 save_param,
+#'                                 else_return = NULL) {
+#'   checkmate::assert_class(gobject, 'giotto')
+#'   checkmate::assert_character(default_save_name)
+#'   checkmate::assert_list(save_param)
+#'
+#'   instr = instructions(gobject)
+#'
+#'   ## output settings detection ##
+#'   # IF setting is NA then the appropriate setting from gobject instructions will
+#'   # be checked and used.
+#'   # IF setting is NOT NA then the provided value will be used directly.
+#'   show_plot = ifelse(is.na(show_plot), readGiottoInstructions(instr, param = 'show_plot'), show_plot)
+#'   save_plot = ifelse(is.na(save_plot), readGiottoInstructions(instr, param = 'save_plot'), save_plot)
+#'   return_plot = ifelse(is.na(return_plot), readGiottoInstructions(instr, param = 'return_plot'), return_plot)
+#' }
+#'
+#'
+#' plot_output_handler_do = function(gplot_out) {
+#'   checkmate::assert_class(gplot_out, 'giottoPlotOutput')
+#'
+#'   ## print plot ##
+#'   if(gplot_out$show_plot) {
+#'     print(gplot_out$plot_object)
+#'   }
+#'
+#'   ## save plot ##
+#'   if(gplot_out$save_plot) {
+#'     do.call('all_plots_save_function',
+#'             c(list(gobject = instr,
+#'                    plot_object = gplot_out$plot_object,
+#'                    default_save_name = default_save_name),
+#'               save_param)
+#'     )
+#'   }
+#'
+#'   ## return plot ##
+#'   if(return_plot) {
+#'     invisible(return(plot_object))
+#'   } else {
+#'     return(else_return)
+#'   }
+#' }
 
 
 

diff --git a/R/plot_save.R → R/aux_save.R b/R/plot_save.R → R/aux_save.R
@@ -2,6 +2,7 @@
 #' @name plot_save
 #' @description
 #' Functions to automatically save plots to directory of interest
+#' @param gobject giotto object or giottoInstructions
 #' @param plot_object ggplot object to plot
 #' @param save_dir directory to save to
 #' @param save_folder folder in save_dir to save to
@@ -28,7 +29,6 @@ NULL
 
 
 #' @describeIn plot_save ggplot saving. ... passes to cowplot::save_plot
-#' @inheritParams data_access_params
 #' @keywords internal
 ggplot_save_function = function(gobject,
                                 plot_object,
@@ -61,7 +61,7 @@ ggplot_save_function = function(gobject,
   if(is.null(save_name)) {
     save_name = default_save_name
     save_name = paste0(plot_count,'-', save_name)
-    options('giotto.plot_count' = plot_count + 1)
+    options('giotto.plot_count' = plot_count + 1L)
   }
   if(is.null(save_format)) save_format = readGiottoInstructions(gobject, param = 'plot_format')
   if(is.null(dpi)) dpi = readGiottoInstructions(gobject, param = 'dpi')
@@ -122,7 +122,6 @@ ggplot_save_function = function(gobject,
 
 
 #' @describeIn plot_save base and general saving. ... passes to grDevices png, tiff, pdf, svg
-#' @inheritParams data_access_params
 #' @keywords internal
 general_save_function = function(gobject,
                                  plot_object,
@@ -240,7 +239,6 @@ general_save_function = function(gobject,
 }
 
 #' @describeIn plot_save wrapper for ggplot and general saving. ... passes to the respective save function
-#' @inheritParams data_access_params
 #' @keywords internal
 all_plots_save_function = function(gobject,
                                    plot_object,