get_condition_biased_comigrations {XINA} | R Documentation

## get_condition_biased_comigrations

### Description

get comigrations that at least one biased cluster is involved in. Biased clusters are defined by

### Usage

    get_condition_biased_comigrations(clustering_result, count_table = NULL,
      selected_conditions, condition_composition, threshold_percent = 50,
      color_for_null = "gray", color_for_highly_matched = "red4",
      cex = 0.7, alpha = 0.3)

### Arguments

`clustering_result` | A list containing XINA clustering results. See xina_clustering
`count_table` | A data frame generated by using count. If count_table is NULL (by default), XINA will consider all the comigrations.
`selected_conditions` | A vector of condition names used in XINA clustering results. The number of selected conditions should be at least two.
`condition_composition` | The resulting data frame of 'plot_condition_compositions'. See plot_condition_compositions.
`threshold_percent` | Default is 50. The percentage threshold for finding condition-biased clusters
`color_for_null` | A color for non-condition-biased comigrations. Default is 'gray'
`color_for_highly_matched` | A color for comigrations that are involved with more than two condition-biased clusters. Default is 'red4'
`cex` | Size of cluster number on block axis. Default if 0.7. See alluvial.
`alpha` | Transparency of alluvia colors. Default is 0.3. See alluvial.

### Value

An alluvial plot displaying comigrations and the data frame containing condition-biased comigrations.

### Examples

    # load XINA example data
    data(xina_example)

    # get a vector of experimental conditions analyzed in the clustering results
    conditions <- as.vector(example_clusters$condition)

    # get condition composition information
    condition_composition <- plot_condition_compositions(example_clusters)

    comigrations_size10 <- alluvial_enriched(example_clusters, conditions, comigration_size=10)
    # Finding condition-biased comigrations by 50% threshold
    condition_biased_comigrations <-
    get_condition_biased_comigrations(clustering_result=example_clusters,
    count_table=comigrations_size10, selected_conditions=conditions,
    condition_composition=condition_composition)

    # Finding condition-biased comigrations by 70% threshold
    condition_biased_comigrations <-
    get_condition_biased_comigrations(clustering_result=example_clusters,
    count_table=comigrations_size10, selected_conditions=conditions,
    condition_composition=condition_composition,
    threshold_percent=70)

[Package XINA version 1.4.0 Index]