Kdreval
commented
3 months ago 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")
Self-explanatory