compare_partitions-ConsensusPartition-method: Compare two partitionings

In jokergoo/cola: A Framework for Consensus Partitioning

Compare two partitionings

Description

Compare two partitionings

Usage

## S4 method for signature 'ConsensusPartition'
compare_partitions(object, object2, output_file, k1 = 2, k2 = 2,
    dimension_reduction_method = "UMAP",
    id_mapping = guess_id_mapping(rownames(object), "org.Hs.eg.db", FALSE),
    row_km1 = ifelse(k1 == 2, 2, 1),
    row_km2 = ifelse(k1 ==2 && k2 == 2, 2, 1),
    row_km3 = ifelse(k2 == 2, 2, 1))

Arguments

object	A ConsensusPartition object.
object2	A ConsensusPartition object.
output_file	The path of the output HTML file. If it is not specified, the report will be opened in the web browser.
k1	Number of subgroups in object.
k2	Number of subgroups in object2.
dimension_reduction_method	Which dimension reduction method to use.
id_mapping	Pass to functional_enrichment,ConsensusPartition-method.
row_km1	Number of k-means groups, see Details.
row_km2	Number of k-means groups, see Details.
row_km3	Number of k-means groups, see Details.

Details

The function produces a HTML report which includes comparisons between two partitioning results.

In the report, there are three heatmaps which visualize A) the signature genes specific in the first partition, B) the signature genes both in the two partitionings and C) the signatures genes specific in the second partition. Argument row_km1, row_km2 and row_km3 control how many k-means groups should be applied on the three heatmaps.

Examples

## Not run: 
data(golub_cola)
require(hu6800.db)
x = hu6800ENTREZID
mapped_probes = mappedkeys(x)
id_mapping = unlist(as.list(x[mapped_probes]))
compare_partitions(golub_cola["ATC:skmeans"], golub_cola["SD:kmeans"], 
    id_mapping = id_mapping)

## End(Not run)

jokergoo/cola documentation built on Feb. 29, 2024, 1:41 a.m.