sample_annotation_to_colors {proBatch} | R Documentation |
Convert the sample annotation data frame to list of colors the list is named as columns included to use in potting functions
sample_annotation_to_colors(sample_annotation, columns_for_plotting = NULL, sample_id_col = "FullRunName", factor_columns = c("MS_batch", "EarTag", "Strain", "Diet", "Sex"), not_factor_columns = "DateTime", numeric_columns = "order", rare_categories_to_other = TRUE, numeric_palette_type = "brewer", granularity = 10)
sample_annotation |
data matrix with:
|
columns_for_plotting |
only consider these columns from sample_annotation |
sample_id_col |
name of the column in sample_annotation file, where the filenames (colnames of the data matrix are found) |
factor_columns |
columns of sample_annotation to be treated as factors. Note that factor and character columns are treated as factors by default. |
not_factor_columns |
don't treat these columns as factors. This can be used to override the default behaviour of considering factors and character columns as factors. |
numeric_columns |
columns of sample_annotation to be treated as continuous numeric values. |
rare_categories_to_other |
if True rare categories will be merged as 'other' |
numeric_palette_type |
palette to be used for numeric values coloring |
granularity |
number of colors to map to the number vector (equally spaced between minimum and maximum) |
list of colors
color_scheme <- sample_annotation_to_colors (example_sample_annotation, factor_columns = c('MS_batch','EarTag', "Strain", "Diet", "digestion_batch", "Sex"), not_factor_columns = 'DateTime', numeric_columns = c('order'))