Comments (1)
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.
Related Issues (20)
- remove ggsci dependency from Description HOT 1
- `heatmap_mutation_frequency_bin` shows pathology even when not specified HOT 1
- Add internal call to prettyOncoplot to convert NA metadata values to literal "NA" string HOT 5
- `heatmap_mutation_frequency_bin` lost rotation of the column title HOT 1
- Error in `prettyOncoplot` HOT 1
- `prettyOncoplot` is missing a step to assign POS/NEG colours HOT 7
- Website/tutorials for GAMBLR.viz HOT 1
- error in `prettyCoOncoplot` HOT 1
- setup github actions for this package
- drop reshape2 dependency
- drop cowplot dependency
- drop plotly dependency
- Develop ggplot2-implemented lollipop plots
- README needs update
- `prettyOncoplot` bugs
- handling of custom colors for numeric annotations HOT 1
- Support custom ordering in prettyForestPlot
- prettyChromoplot does not take projection/genome_build as argument HOT 1
- prettyChromoplot doesn't allow labelling of cytobands HOT 2
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from gamblr.viz.