inst/tests/testthat/test-9pfplotting.R

In reptalex/phylofactor: phylofactor

context('Testing phylofactor plotting tools')
options(warn=-1)
set.seed(2)
data("FTmicrobiome",package = 'phylofactor')
tree <- FTmicrobiome$tree
Taxonomy <- FTmicrobiome$taxonomy
tree <- ape::drop.tip(tree,setdiff(tree$tip.label,sample(tree$tip.label,20)))

Taxonomy <- Taxonomy[match(tree$tip.label,Taxonomy[,1]),]
X <- as.factor(c(rep(0,5),rep(1,5)))

### Simulate data ###
Factornodes <- c(37,27)
sigClades <- list(c(16,17),c(6,7,8,9,10,11,12,13,14,15))

Data <- matrix(rlnorm(20*10,meanlog = 8,sdlog = .5),nrow=20)
rownames(Data) <- tree$tip.label
colnames(Data) <- X
Data[sigClades[[1]],X==0] <- Data[sigClades[[1]],X==0]*9
Data[sigClades[[2]],X==1] <- Data[sigClades[[2]],X==1]*14
Bins <- bins(G=sigClades,set=1:20)[c(3,2,1)]

invisible(capture.output(pf <- PhyloFactor(Data,tree,X,nfactors=3)))

# test_that('pf.plot does not error',
          # expect_error(pf.plot(pf),NA))
# test_that('binPhyloPlot dimension=3 does not error',
          # expect_error(binPhyloPlot(pf,factor = 3),NA))
test_that('pf.tree does not error',
          expect_error(pf.tree(pf),NA))
# test_that('ColorTaxa works',
          # expect_error(ColorTaxa(tree,Taxonomy,legend = T,outputlegend = T),NA))
options(warn=0)