https://github.com/erblast/parcats/issues/18

.github/workflows/pkgdown.yml → .github/workflows/pkgdown.yaml

@@ -4,12 +4,13 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -22,7 +23,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -34,22 +35,15 @@ jobs:
         with:
           extra-packages: any::pkgdown, local::.
           needs: website
-      - name: Install dependencies
-        run: |
-          install.packages("devtools")
-          system("git clone https://github.com/erblast/parcats.git")
-          devtools::install("parcats/", dependencies = TRUE)
-        shell: Rscript {0}
-
 
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages
-          folder: docs
+          folder: docs

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

.gitignore

@@ -7,4 +7,5 @@ revdep/
 inst/doc
 docker.sh
 docs/
-.DS_Store
+.DS_Store
+docs

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: parcats
 Title: Interactive Parallel Categories Diagrams for 'easyalluvial'
-Version: 0.0.5
+Version: 0.1.0
 Authors@R: person( "Bjoern", "Koneswarakantha", role = c("aut","cre"), email = "datistics@gmail.com", comment = c(ORCID = "0000-0003-4585-7799") )
 URL: https://erblast.github.io/parcats/
 BugReports: https://github.com/erblast/parcats/issues/
@@ -22,9 +22,9 @@ Suggests:
     spelling,
     plotly,
     shiny
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Imports:
-  easyalluvial (>= 0.2.1.0),
+  easyalluvial (>= 0.4.0),
   tidyr (>= 1.0.0),
   dplyr,
   purrr,

NEWS.md

@@ -1,3 +1,6 @@
+# parcats 0.1.0
+* adapt to easyalluvial v0.4.0 and ggplot2 v4.0.0
+
 # parcats 0.0.5
 * update vignette
 * fix documentation

R/parcats.R

@@ -13,7 +13,7 @@ if(getRversion() >= "2.15.1"){
 
 trace_hist_all = function(p, data_input){
 
-  vars = p$data$x %>% levels()
+  vars = manip_get_ggplot_data(p)$x %>% levels()
 
   traces = list()
 
@@ -24,7 +24,7 @@ trace_hist_all = function(p, data_input){
     if(! is_pred){
       is_num = is.numeric( data_input[[var]] )
     }else{
-      var_pred = names(data_input)[! names(data_input) %in% names(p$alluvial_params$dspace) ]
+      var_pred = names(data_input)[! names(data_input) %in% names(attr(p, "alluvial_params")$dspace) ]
       if(length(var_pred) > 1){
         stop( paste('\n"data_input" should only contain explanatory and response variables, so response variable can be inferred.
                   \nPotential response variables:', paste( var_pred, collapse = ', ')
@@ -46,7 +46,7 @@ trace_hist_all = function(p, data_input){
 }
 
 trace_rug_all = function(p, data_input){
-  vars = p$data$x %>% levels()
+  vars = manip_get_ggplot_data(p)$x %>% levels()
 
   traces = list()
 
@@ -62,7 +62,7 @@ trace_rug_all = function(p, data_input){
 
 trace_rug = function(p, data_input, var){
 
-  vars = p$data$x %>% levels
+  vars = manip_get_ggplot_data(p)$x %>% levels
 
   is_num = is.numeric(data_input[[var]])
 
@@ -100,7 +100,7 @@ trace_hist_mod = function(p, data_input, var){
 
   df = p_hist$data
 
-  vars = p$data$x %>% levels
+  vars = manip_get_ggplot_data(p)$x %>% levels
 
   values = data_input[[var]]
 
@@ -125,15 +125,15 @@ trace_hist_mod = function(p, data_input, var){
   trace_var = list(trace_var)
   names(trace_var) <- paste0( var, '_dens')
 
-  lines_at = p$alluvial_params$dspace[[var]] %>%
+  lines_at = attr(p, "alluvial_params")$dspace[[var]] %>%
     unique() %>%
     sort()
 
   # we have to rejoin with fill labels
   # labels need to be consistent {var}_{fill_label} so that we 
   # can track the traces
 
-  fill_labels = p$data %>%
+  fill_labels = manip_get_ggplot_data(p) %>%
     filter( x == var) %>%
     select( value, fill_value) %>%
     distinct() %>%
@@ -172,15 +172,15 @@ trace_hist_num = function(p, data_input, var){
 
   df = p_hist$data
 
-  vars = p$data$x %>% levels
+  vars = manip_get_ggplot_data(p)$x %>% levels
 
   if(var == 'pred'){
 
     # we have to rejoin with fill labels
     # labels need to be consistent {var}_{fill_label} so that we 
     # can track the traces
 
-    fill_labels = p$data %>%
+    fill_labels = manip_get_ggplot_data(p) %>%
       filter( x == 'pred') %>%
       select(fill, value, fill_value) %>%
       mutate( rwn = as.numeric(fill) ) %>%
@@ -194,7 +194,7 @@ trace_hist_num = function(p, data_input, var){
       left_join( fill_labels, by = 'rwn')
   }
 
-  if( p$alluvial_type == 'model_response' & var != 'pred'){
+  if( attr(p, "alluvial_type") == 'model_response' & var != 'pred'){
     return( trace_hist_mod(p, data_input, var) )
   }
 
@@ -227,7 +227,7 @@ trace_hist_cat = function(p, data_input, var){
 
   p_hist = easyalluvial::plot_hist(var = var, p = p, data_input = data_input)
 
-  df_label = p$data %>%
+  df_label = manip_get_ggplot_data(p) %>%
     filter( x == var ) %>%
     mutate( value = fct_drop(value) ) %>%
     select( value ) %>%
@@ -260,7 +260,7 @@ trace_hist_cat = function(p, data_input, var){
 
   lvl = levels(df[[var]])
 
-  vars = p$data$x %>% levels
+  vars = manip_get_ggplot_data(p)$x %>% levels
 
   df = df %>%
     mutate( var_key = fct_relevel(var_key, lvl) ) %>%
@@ -287,7 +287,7 @@ trace_imp = function(p, data_input, truncate_at = 50, color = 'darkgrey'){
 
   p_imp = easyalluvial::plot_imp(p, data_input, truncate_at, color )
 
-  df = p_imp$data
+  df = manip_get_ggplot_data(p_imp)
 
   if( ! 'const_values' %in% names(df) ){
     df$const_values = NA
@@ -297,7 +297,7 @@ trace_imp = function(p, data_input, truncate_at = 50, color = 'darkgrey'){
     mutate_if( is.factor, as.character ) %>%
     arrange( perc ) %>%
     mutate( fill = ifelse(plotted == 'n', 'lightgrey', color)
-            , method = p$alluvial_params$method 
+            , method = attr(p, "alluvial_params")$method 
             , text = case_when( plotted == 'y' ~ 'alluvial'
                                 , method == 'pdp' ~ 'pdp'
                                 , TRUE ~ paste('fixed:', const_values) ) ) %>%
@@ -334,8 +334,8 @@ trace_parcats = function(p
                          , tickfont
                          ){
 
-  if(p$alluvial_type == 'model_response'){
-    df = p$data %>%
+  if(attr(p, "alluvial_type") == 'model_response'){
+    df = manip_get_ggplot_data(p) %>%
       arrange( desc(value) ) %>%
       mutate(value_str = as.character(value)
               , value_str = ifelse( x != 'pred', str_split(value_str, '\\\n'), value_str)
@@ -345,15 +345,15 @@ trace_parcats = function(p
               , value = value_str) %>%
       select( - value_str)
   }else{
-    df = p$data
+    df = manip_get_ggplot_data(p)
   }
 
   df = df %>%
     select( - fill_value, - fill ) %>%
     spread(x, value) %>%
     arrange(alluvial_id)
 
-  if (p$alluvial_params$fill_by == "values") {
+  if (attr(p, "alluvial_params")$fill_by == "values") {
     stop("fill_by = 'values' not supported in parcats")
   }
 
@@ -482,7 +482,7 @@ create_layout_hist = function(trace_hist
 
 map_trace = function(p, trace_hist){
 
-  df = p$data %>%
+  df = manip_get_ggplot_data(p) %>%
     mutate( x_value = map2_chr(x, value, function(x,y) paste0(x,'_' ,y) )
             , trace_number = map(x_value, ~ which(names(trace_hist) == . ) )
             , trace_number = map_int(trace_number, ~ ifelse( is_empty(.), NA, .)  ) ) %>%
@@ -641,9 +641,9 @@ parcats <- function(p, marginal_histograms = TRUE, data_input = NULL
     stop('data_input required if marginal_histograms == TRUE')
   }
 
-  if( imp == TRUE & is.null(data_input) & p$alluvial_type == 'model_response' ){
+  if( imp == TRUE & is.null(data_input) & attr(p, "alluvial_type") == 'model_response' ){
     stop('data_input required if imp == TRUE')
-  }else if(p$alluvial_type != 'model_response' | ! imp ){
+  }else if(attr(p, "alluvial_type") != 'model_response' | ! imp ){
     imp = FALSE
     offset_imp = 1
   }
@@ -654,7 +654,7 @@ parcats <- function(p, marginal_histograms = TRUE, data_input = NULL
     domain = list( y = c(0, 1) )
   }
 
-  if( imp & p$alluvial_type == 'model_response' ){
+  if( imp & attr(p, "alluvial_type") == 'model_response' ){
     domain$x = c(0, offset_imp - 0.05 )
     traces_imp = trace_imp(p, data_input, truncate_at = 50, color = 'darkgrey')
   }else{
@@ -718,7 +718,7 @@ parcats <- function(p, marginal_histograms = TRUE, data_input = NULL
 
     p_imp = easyalluvial::plot_imp(p, data_input)
 
-    max_perc = p_imp$data$perc %>% max()
+    max_perc = manip_get_ggplot_data(p_imp)$perc %>% max()
 
     for( i in seq(1, length(traces_imp) ) ){
       l = list( xref = 'x99'