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Kdreval avatar Kdreval commented on September 27, 2024

Current status indicates the issue that needs to be addressed:

❯ checking for code/documentation mismatches ... WARNING
  Codoc mismatches from documentation object 'heatmap_mutation_frequency_bin':
  heatmap_mutation_frequency_bin
    Code: function(regions_list = NULL, regions_bed = NULL,
                   these_samples_metadata = NULL, these_sample_ids =
                   NULL, this_seq_type = c("genome", "capture"),
                   maf_data, mut_freq_matrix, projection = "grch37",
                   region_padding = 1000, drop_unmutated = FALSE,
                   metadataColumns = c("pathology"), sortByColumns =
                   NULL, expressionColumns = NULL, orientation =
                   "sample_rows", skip_regions, only_regions,
                   customColours = NULL, naColour = "white",
                   backgroundColour = "grey90", slide_by = 100,
                   window_size = 500, min_count_per_bin = 0,
                   min_bin_recurrence = 5, min_mut_tumour = 0,
                   region_fontsize = 8, cluster_rows_heatmap = FALSE,
                   cluster_cols_heatmap = FALSE, show_gene_colours =
                   FALSE, label_regions_by = "name", label_regions_rotate
                   = 0, legend_row = 3, legend_col = 3, legend_direction
                   = "horizontal", legendFontSize = 10, legend_side =
                   "bottom", return_heatmap_obj = FALSE,
                   from_indexed_flatfile = TRUE, mode = "slms-3")
    Docs: function(regions_list = NULL, regions_bed = NULL,
                   these_samples_metadata = NULL, these_sample_ids =
                   NULL, this_seq_type = c("genome", "capture"),
                   maf_data, mut_freq_matrix, projection = "grch37",
                   region_padding = 1000, drop_unmutated = FALSE,
                   metadataColumns = c("pathology"), sortByColumns =
                   c("pathology"), expressionColumns = NULL, orientation
                   = "sample_rows", skip_regions, only_regions,
                   customColours = NULL, backgroundColour = "grey90",
                   slide_by = 100, window_size = 500, min_count_per_bin =
                   0, min_bin_recurrence = 5, min_mut_tumour = 0,
                   region_fontsize = 8, cluster_rows_heatmap = FALSE,
                   cluster_cols_heatmap = FALSE, show_gene_colours =
                   FALSE, label_regions_by = "name", label_regions_rotate
                   = 0, legend_row = 3, legend_col = 3, legend_direction
                   = "horizontal", legendFontSize = 10, legend_side =
                   "bottom", return_heatmap_obj = FALSE,
                   from_indexed_flatfile = TRUE, mode = "slms-3")
    Argument names in code not in docs:
      naColour
    Mismatches in argument names (first 3):
      Position: 18 Code: naColour Docs: backgroundColour
      Position: 19 Code: backgroundColour Docs: slide_by
      Position: 20 Code: slide_by Docs: window_size
    Mismatches in argument default values:
      Name: 'sortByColumns' Code: NULL Docs: c("pathology")

from gamblr.viz.

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