get_comigrations_by_name: get_comigrations_by_name

In langholee/XINA: Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis

Description

'get_comigrations_by_name' finds proteins comigrated with the given proteins

Usage

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

# 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])

langholee/XINA documentation built on March 17, 2020, 5:23 p.m.