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Filter by factor levels

Source: R/filter_venn_class.R
filter_venn.Rd

Removes (or includes) annotations such that the named column excludes (or includes) the specified intersection levels. Supports any number of groups using intersection-based filtering. If no levels are specified, all available intersection levels will be returned for inspection. If invalid levels are specified, a warning will be shown with the list of valid levels.

Usage

filter_venn(
  factor_name,
  group_column = NULL,
  tables = NULL,
  filter = NULL,
  mode = "include",
  ...
)

Arguments

factor_name

(character) The name of the column(s) in the annotation_source to generate intersection groups from. Supports any number of columns for intersection-based filtering.

group_column

(character, NULL) The name of the column in the annotation_source to create groups from in the Venn diagram. This parameter is ignored if !is.null(tables), as each table is considered to be a group. This parameter is also ignored if more than one factor_name is provided, as each column is considered a group. The default is NULL.

tables

(list, NULL) A list of annotation_sources to generate the venn groups from. If the only table of interest is the table coming in from model_apply then set tables = NULL and use group_column. The default is NULL.

filter

(function, NULL) A function to filter intersections based on their properties. The function should take region_data as input and return a logical vector indicating which intersections to keep. Use upset_intersections(), upset_min_size(), upset_min_groups(), upset_max_groups(), or create custom filter functions. The default is NULL.

mode

(character) Filter mode. Allowed values are limited to the following:

  • "include": Only items that appear in the filtered intersections are kept in the output.

  • "exclude": Items that appear in the filtered intersections are removed from the output.

The default is "include".

...

Additional slots and values passed to struct_class.

Value

A filter_venn object with the following output slots:

filtered(annotation_source) Annotation_source after filtering.
flags(data.frame) A list of flags indicating which annotations were removed.

Inheritance

A filter_venn object inherits the following struct classes:

[filter_venn] -> [model] -> [struct_class]

Examples

M <- filter_venn(
        factor_name = "V1",
        group_column = NULL,
        tables = NULL,
        filter = NULL,
        mode = "include")