get_comigrations_by_name: get_comigrations_by_name

Description Usage Arguments Value Examples

View source: R/coregulstions.R

Description

'get_comigrations_by_name' finds proteins comigrated with the given proteins

Usage

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get_comigrations_by_name(clustering_result, selected_conditions,
  protein_list, cex = 0.7, alpha = 0.3)

Arguments

clustering_result

A list containing XINA clustering results. See xina_clustering

selected_conditions

A vector of condition names used in XINA clustering results. The number of selected conditions should be at least two.

protein_list

A vector containing gene names.

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 comigrations of the input proteins

Examples

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# load XINA example data
data(xina_example)

# the clustering result table
all_proteins  <- as.character(example_clusters$aligned$`Gene name`)
# get a vector of experimental conditions analyzed in the clustering results
classes <- as.vector(example_clusters$condition)

comigrated_prots_all <- get_comigrations_by_name(example_clusters, classes, all_proteins[1:3])

XINA documentation built on Nov. 8, 2020, 5:32 p.m.