Merge pull request #87 from drieslab/dev

GiottoVisuals 0.2.6
drieslab · Oct 27, 2024 · a37b74d · a37b74d
2 parents 1d2d7f5 + eeddaf5
commit a37b74d
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Showing 72 changed files with 10,485 additions and 9,177 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -8,3 +8,4 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+testout
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -52,9 +52,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
-          - { os: macOS-latest, r: '4.3', bioc: '3.18'}
-          - { os: windows-latest, r: '4.3', bioc: '3.18'}
+          - { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
+          - { os: macOS-latest, r: '4.4', bioc: '3.19'}
+          - { os: windows-latest, r: '4.4', bioc: '3.19'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -105,16 +105,16 @@ jobs:
         uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
         uses: actions/cache@v4
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-
 
       # - name: Install Linux system dependencies
       #   if: runner.os == 'Linux'
@@ -303,7 +303,7 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-results
+          name: ${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-results
           path: check
 
 

diff --git a/.github/workflows/covr.yml b/.github/workflows/covr.yml
@@ -4,7 +4,7 @@ name: code coverage
 
 on:
   push:
-    branches: [ "dev2" ]
+    branches: [ "dev" ]
   pull_request:
     types: closed
     branches: [ "main" ]

diff --git a/.github/workflows/dev_check.yml b/.github/workflows/dev_check.yml
@@ -10,7 +10,7 @@
 name: Dev Workflow - Test and check
 on:
   push:
-    branches: [ "dev2" ]
+    branches: [ "dev" ]
 
 permissions:
   contents: read

diff --git a/.github/workflows/lintr.yml b/.github/workflows/lintr.yml
@@ -12,10 +12,10 @@ name: lintr
 
 on:
   push:
-    branches: [ "dev2" ]
+    branches: [ "dev" ]
   pull_request:
     # The branches below must be a subset of the branches above
-    branches: [ "dev2" ]
+    branches: [ "dev" ]
   schedule:
     - cron: '16 20 * * 2'
 

diff --git a/.gitignore b/.gitignore
@@ -7,3 +7,4 @@ inst/doc
 .vscode/*
 .Rprofile
 docs
+testout
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: GiottoVisuals
 Title: Visuals for the Giotto spatial biology analysis ecosystem
-Version: 0.2.4
+Version: 0.2.6
 Authors@R: c(
 	person("Ruben", "Dries", email = "[email protected]",
 		 role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),
@@ -23,23 +23,19 @@ BugReports: https://github.com/drieslab/Giotto/issues
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 Depends:
-    base (>= 4.1.0),
-    utils (>= 4.1.0),
-    R (>= 4.1.0),
+    R (>= 4.4.1)
 Imports:
     checkmate,
     colorRamp2,
     cowplot (>= 0.9.4),
     data.table,
     ggplot2 (>= 3.1.1),
-    GiottoUtils (>= 0.1.8),
-    GiottoClass (>= 0.3.1),
+    GiottoUtils (>= 0.1.12),
+    GiottoClass (>= 0.3.6),
     ggrepel,
     igraph (>= 1.2.4.1),
     methods,
     plotly,
-    RColorBrewer (>= 1.1-2),
-    reshape2,
     scales (>= 1.0.0),
     scattermore,
     stats,
@@ -53,14 +49,14 @@ Suggests:
     ggsci,
     GiottoData,
     htmlwidgets,
-    Matrix,
     networkD3,
     NineteenEightyR,
     nord,
     palr,
     palettetown,
     png,
     rcartocolor,
+    RColorBrewer (>= 1.1-2),
     remotes,
     scatterpie,
     tiff,
@@ -86,19 +82,22 @@ Collate:
     'generics.R'
     'gg_annotation_raster.R'
     'gg_info_layers.R'
+    'gg_param.R'
     'gg_settings.R'
     'globals.R'
     'gstop.R'
     'mixcolor.R'
     'plot_dendrogram.R'
+    'plot_dotplot.R'
     'plot_heatmap.R'
     'plot_sankey.R'
     'plot_scatter.R'
     'plot_violin.R'
     'spatialDE_visuals.R'
     'suite_reexports.R'
-    'vis_spatial.R'
+    'vis_spatial_gg.R'
     'vis_spatial_in_situ.R'
+    'vis_spatial_plotly.R'
     'viz_spatial_network.R'
     'zzz.R'
 biocViews: Software, Technology, Spatial

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,10 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(print,giotto_plot_save_param)
 export("sankeyLabel<-")
 export(FSV_show)
 export(addGiottoImageToSpatPlot)
 export(all_plots_save_function)
 export(colorRamp2)
+export(combine_aes)
 export(create_cluster_dendrogram)
 export(dimCellPlot)
 export(dimCellPlot2D)
@@ -14,15 +16,18 @@ export(dimGenePlot3D)
 export(dimPlot)
 export(dimPlot2D)
 export(dimPlot3D)
+export(dotPlot)
 export(expand_feature_info)
 export(geom_label_repel)
 export(geom_text_repel)
 export(getColors)
 export(getDistinctColors)
 export(getRainbowColors)
 export(get_continuous_colors)
+export(gg_param)
 export(gg_simple_scatter)
 export(giottoSankeyPlan)
+export(gpsparam)
 export(mixHSV)
 export(mixRGB)
 export(pal_names)
@@ -39,6 +44,7 @@ export(plotTSNE_3D)
 export(plotUMAP)
 export(plotUMAP_2D)
 export(plotUMAP_3D)
+export(plot_grid)
 export(plot_output_handler)
 export(plotly_axis_scale_2D)
 export(plotly_axis_scale_3D)
@@ -89,6 +95,7 @@ export(spatPlot)
 export(spatPlot2D)
 export(spatPlot3D)
 export(subsetSankeySet)
+export(theme_dark2)
 export(violinPlot)
 exportClasses(giottoSankeyPlan)
 exportMethods("+")
@@ -98,7 +105,6 @@ exportMethods(sankeyPlot)
 exportMethods(sankeyRelate)
 import(GiottoClass)
 import(GiottoUtils)
-import(RColorBrewer)
 import(cowplot)
 import(ggplot2)
 import(ggrepel)
@@ -108,6 +114,7 @@ importClassesFrom(data.table,data.table)
 importFrom(GiottoUtils,getDistinctColors)
 importFrom(GiottoUtils,getRainbowColors)
 importFrom(colorRamp2,colorRamp2)
+importFrom(cowplot,plot_grid)
 importFrom(data.table,dcast)
 importFrom(data.table,dcast.data.table)
 importFrom(ggrepel,geom_label_repel)
@@ -118,7 +125,6 @@ importFrom(methods,setGeneric)
 importFrom(methods,setMethod)
 importFrom(methods,slot)
 importFrom(plotly,add_segments)
-importFrom(reshape2,melt)
 importFrom(scales,rescale_mid)
 importFrom(stats,cov)
 importFrom(stats,var)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,19 @@
+# GiottoVisuals 0.2.6 (2024/10/27)
+
+## new
+- `combine_aes()` for combining ggplot2 mappings in a last item wins manner. Allows more than 2 aes to be combined at the same time and provides an optional informative warning
+- `gg_params()` for combining and sorting ggplot2 mappings, toplevel params, and data into an arg list for plotting.
+
+
+# GiottoVisuals 0.2.5 (2024/09/27)
+
+## new
+- `gpsparam()` for generating an object containing plot saving parameters
+- `cowplot::plot_grid()` re-exported
+- `dotPlot()` visualization
+
+## bug fixes
+- fix `coord_fix_ratio` passing in `spatFeatPlot2D()` [#972](https://github.com/drieslab/Giotto/issues/972) by kaizen89
 
 # GiottoVisuals 0.2.4 (2024/07/26)
 

diff --git a/R/aux_output.R b/R/aux_output.R
@@ -25,9 +25,9 @@
 #' @examples
 #' g <- GiottoData::loadGiottoMini("vizgen")
 #' g_spatplot <- spatPlot2D(g, return_plot = TRUE)
-#' 
+#'
 #' plot_output_handler(g, plot_object = g_spatplot, save_plot = FALSE)
-#' 
+#'
 #' @export
 plot_output_handler <- function(
         gobject,
@@ -41,22 +41,12 @@ plot_output_handler <- function(
     checkmate::assert_class(gobject, "giotto")
 
     ## output settings detection ##
-    # IF setting is NULL then the appropriate setting from gobject instructions
-    # will be checked and used.
-    # IF setting is NOT NULL then the provided value will be used directly.
-    show_plot <- ifelse(is.null(show_plot),
-        readGiottoInstructions(gobject, param = "show_plot"),
-        show_plot
-    )
-    save_plot <- ifelse(is.null(save_plot),
-        readGiottoInstructions(gobject, param = "save_plot"),
-        save_plot
-    )
-    return_plot <- ifelse(is.null(return_plot),
-        readGiottoInstructions(gobject, param = "return_plot"),
-        return_plot
-    )
+    show_plot <- show_plot %null% instructions(gobject, param = "show_plot")
+    save_plot <- save_plot %null% instructions(gobject, param = "save_plot")
+    return_plot <- return_plot %null%
+        instructions(gobject, param = "return_plot")
 
+    ## handle outputs --------------------------------------------------- ##
 
     ## print plot ##
     if (show_plot) {
@@ -67,18 +57,14 @@ plot_output_handler <- function(
     if (save_plot) {
         checkmate::assert_character(default_save_name)
         checkmate::assert_list(save_param)
-
-        do.call(
-            "all_plots_save_function",
-            c(
-                list(
-                    gobject = gobject,
-                    plot_object = plot_object,
-                    default_save_name = default_save_name
-                ),
-                save_param
-            )
+
+        data_param <- list(
+            gobject = gobject,
+            plot_object = plot_object,
+            default_save_name = default_save_name
         )
+
+        do.call("all_plots_save_function", args = c(data_param, save_param))
     }
 
     ## return plot ##
@@ -103,9 +89,9 @@ plot_output_handler <- function(
 #     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.
@@ -121,12 +107,12 @@ plot_output_handler <- function(
 
 # 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$save_plot) {
 #         do.call('all_plots_save_function',
@@ -136,7 +122,7 @@ plot_output_handler <- function(
 #                   save_param)
 #         )
 #     }
-#     
+#
 #     ## return plot ##
 #     if(return_plot) {
 #         invisible(return(plot_object))
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,3 +8,4 @@ @@
     ^docs$
     ^pkgdown$
     ^\.github$
+    testout