tests/testthat/test_functions.R

In conos: Clustering on Network of Samples

## following the walkthrough tutorial, walkthrough.md

library(conos)
library(pagoda2)

con <- Conos$new(small_panel.preprocessed, n.cores=1)

test_that("check Conos object, samples", {
	expect_equal(length(con$samples), 2)
})


test_that("check getDatasetPerCell()", {
	expect_equal(length(con$getDatasetPerCell()), 59)
})


test_that("check getJointCountMatrix()", {
	expect_equal(length(con$getJointCountMatrix()), 59000)
})


## warnings due to small panel
suppressWarnings(con$buildGraph(ncomps=25))#
suppressWarnings(con$findCommunities(method=leiden.community)) 
suppressWarnings(con$embedGraph(alpha=0.001, sgd_batched=1e8))


test_that("check Conos object, output of Leiden clustering", {
	expect_equal(length(con$clusters$leiden$groups), 59)
	expect_equal(length(con$clusters$leiden$result), 6)
})


## warnings due to small panel
suppressWarnings(con$buildGraph(ncomps=25))
suppressWarnings(con$findCommunities(method = igraph::walktrap.community, steps=7))
suppressWarnings(con$embedGraph(alpha=0.001, sgd_batched=1e8))


test_that("check Conos object, output of igraph walktrap clustering", {
	expect_equal(length(con$clusters$walktrap$groups), 59)
	expect_equal(length(con$clusters$walktrap$result), 2)
})