Recreating the dynbenchmark figures

library(funkyheatmap)
library(kableExtra)

data("dynbenchmark_data")

data <- dynbenchmark_data$data
print(data[,1:12])
#> # A tibble: 51 × 12
#>    id    metho…¹ metho…² tool_id metho…³ metho…⁴ metho…⁵ metho…⁶ metho…⁷ wrapp…⁸
#>    <chr> <chr>   <chr>   <chr>   <chr>   <chr>   <chr>   <list>  <chr>   <list> 
#>  1 paga  PAGA    tool    paga    Python  https:… <NA>    <list>   <NA>   <chr>  
#>  2 race… RaceID… tool    raceid… R       https:… <NA>    <list>   <NA>   <chr>  
#>  3 slic… SLICER  tool    slicer  R       https:… GPL-2   <list>   <NA>   <chr>  
#>  4 slin… Slings… tool    slings… R       https:… Artist… <list>   <NA>   <chr>  
#>  5 paga… PAGA T… tool    paga    Python  https:… <NA>    <list>  "This … <chr>  
#>  6 proj… Projec… tool    slings… R       https:… Artist… <list>   <NA>   <chr>  
#>  7 mst   MST     offthe… mst     R       <NA>    <NA>    <list>   <NA>   <chr>  
#>  8 mono… Monocl… tool    monocle R       https:… Artist… <list>   <NA>   <chr>  
#>  9 mono… Monocl… tool    monocle R       https:… Artist… <list>   <NA>   <chr>  
#> 10 pcre… pCreode tool    pcreode Python  https:… GPL-2   <list>   <NA>   <chr>  
#> # … with 41 more rows, 2 more variables: wrapper_input_optional <list>,
#> #   wrapper_type <chr>, and abbreviated variable names ¹​method_name,
#> #   ²​method_source, ³​method_platform, ⁴​method_url, ⁵​method_license,
#> #   ⁶​method_authors, ⁷​method_description, ⁸​wrapper_input_required

preview_cols <- c(
  "id",
  "method_source",
  "method_platform",
  "benchmark_overall_norm_correlation",
  "benchmark_overall_norm_featureimp_wcor",
  "benchmark_overall_norm_F1_branches",
  "benchmark_overall_norm_him",
  "benchmark_overall_overall"
)
kable(data[,preview_cols])

g <- funky_heatmap(data[,preview_cols])
#> ℹ No column info was provided, assuming all columns in `data` are to be plotted.
#> ℹ Column info did not contain column `name`, using `id` to generate it.
#> ℹ Column info did not contain information on which columns to plot, inferring from `data` types.
#> ℹ Column info did not contain group information, assuming columns are ungrouped.
#> ℹ Column info did not contain a column called 'palette', generating palettes based on the 'geom' column.
#> ℹ Column info did not contain a column called 'width', generating options based on the 'geom' column.
#> ℹ Column info did not contain a column called 'legend', generating options based on the 'geom' column.
#> ℹ No row info was provided, assuming all rows in `data` are to be plotted.
#> ℹ Row info did not contain group information, assuming rows are ungrouped.
#> ℹ No palettes were provided, trying to automatically assign palettes.
#> ℹ Palette named 'numerical_palette' was not defined. Assuming palette is numerical. Automatically selected palette 'Blues'.

g

column_info <- dynbenchmark_data$column_info
kable(column_info)

g <- funky_heatmap(data, column_info = column_info)
#> ℹ No row info was provided, assuming all rows in `data` are to be plotted.
#> ℹ Row info did not contain group information, assuming rows are ungrouped.
#> ℹ No column groups was provided, deriving from column info.
#> ℹ Column groups did not contain a column called 'palette'. Assuming no colour scales need to be used.
#> ℹ Column groups did not contain a column called 'level1'. Using `column_info$group` as a makeshift column group name.
#> ℹ No palettes were provided, trying to automatically assign palettes.
#> ℹ Palette named 'overall' was not defined. Assuming palette is numerical. Automatically selected palette 'Blues'.
#> ℹ Palette named 'benchmark' was not defined. Assuming palette is numerical. Automatically selected palette 'Reds'.
#> ℹ Palette named 'scaling' was not defined. Assuming palette is numerical. Automatically selected palette 'YlOrBr'.
#> ℹ Palette named 'stability' was not defined. Assuming palette is numerical. Automatically selected palette 'Greens'.
#> ℹ Palette named 'qc' was not defined. Assuming palette is numerical. Automatically selected palette 'Greys'.
#> ℹ Palette named 'error_reasons' was not defined. Assuming palette is categorical. Automatically selected palette 'Set3'.
#> ℹ Palette named 'white6black4' was not defined. Assuming palette is numerical. Automatically selected palette 'Blues'.

g
#> Warning: Removed 17 rows containing missing values (`geom_rect()`).
#> Warning: Removed 1 rows containing missing values (`geom_text()`).

column_groups <- dynbenchmark_data$column_groups
kable(column_groups)

row_info <- dynbenchmark_data$row_info
kable(row_info)

row_groups <- dynbenchmark_data$row_groups
kable(row_groups)

palettes <- dynbenchmark_data$palettes
print(palettes)
#> # A tibble: 7 × 2
#>   palette       colours    
#>   <chr>         <list>     
#> 1 overall       <chr [101]>
#> 2 benchmark     <chr [101]>
#> 3 scaling       <chr [101]>
#> 4 stability     <chr [101]>
#> 5 qc            <chr [101]>
#> 6 error_reasons <chr [4]>  
#> 7 white6black4  <chr [10]>

g <- funky_heatmap(
  data = data,
  column_info = column_info,
  column_groups = column_groups,
  row_info = row_info,
  row_groups = row_groups,
  palettes = palettes,
  col_annot_offset = 3.2
)

g
#> Warning: Removed 17 rows containing missing values (`geom_rect()`).
#> Warning: Removed 1 rows containing missing values (`geom_text()`).

ggsave("path_to_plot.pdf", g, device = cairo_pdf, width = g$width, height = g$height)