Compare Two Partitioning Results

Zuguang Gu ()

2024-02-27

Source: vignettes/compare_partitions.Rmd

cola allows to perform multiple partitioning methods in paralle. Different partitioning methods might give different partitions. Here the function compare_partitions() can compare two partitioning results by a HTML report.

We take golub_cola as an example which contains consensus partitioning results of the Golub dataset.

library(cola)
data(golub_cola)

Basically we can directly provide two ConsensusPartition objects to this function:

compare_partitions(golub_cola["ATC:skmeans"], golub_cola["SD:kmeans"])

compare_partitions() generates a HTML file, and it automatically opens it in the web browser. If the matrix rows are genes with IDs as Ensemble IDs, RefSeq IDs or gene symbols, functional enrichment will also be applied to the signature genes under the two sets of partitions to see which is more biological meaningful.

Genes in golub_cola have microarray probe IDs, so here we need to provide a gene ID mapping vector which maps probe IDs to Entrez IDs, as what is done in the following code:

require(hu6800.db)
## Warning: package 'S4Vectors' was built under R version 4.3.2
x = hu6800ENTREZID
mapped_probes = mappedkeys(x)
id_mapping = unlist(as.list(x[mapped_probes]))
head(id_mapping)
##     A28102_at   AB000114_at   AB000115_at   AB000220_at AB000381_s_at   AB000409_at 
##        "2556"        "4958"       "10964"       "10512"        "2765"        "8569"

Note if the ID mapping is not provided, the functional enrichment will not be applied.

compare_partitions(golub_cola["ATC:skmeans"], golub_cola["SD:kmeans"], 
    id_mapping = id_mapping, output_file = "compare_partitions_example.html")
## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

## Warning: 'mode(bg)' differs between new and previous
##   ==> NOT changing 'bg'

An example output can be found in this link.