context("test estimation of gene ages")
test_that("test estimation of gene ages", {
library(dplyr)
data("fullProcessedProfile", package="PhyloProfile")
rankName <- "class"
refTaxon <- "Mammalia"
var1Cutoff <- c(0,1)
var2Cutoff <- c(0,1)
percentCutoff <- c(0,1)
taxonIDs <- levels(as.factor(fullProcessedProfile$ncbiID))
sortedInputTaxa <- sortInputTaxa(
taxonIDs, rankName, refTaxon, NULL
)
taxaCount <- sortedInputTaxa %>% dplyr::count(supertaxon)
geneAge <- estimateGeneAge(
fullProcessedProfile, taxaCount,
rankName, refTaxon,
var1Cutoff, var2Cutoff, percentCutoff
)
expect_true(
geneAge$age[geneAge$geneID == "103479at6656"] == "08_Eukaryota"
)
})
test_that("test plotting gene age plot", {
geneAgeDf <- data.frame(
geneID = c("OG_1017", "OG_1019"),
cat = c("0000001", "0000001"),
age = c("07_LUCA", "07_LUCA"),
stringsAsFactors = FALSE
)
plotDf <- geneAgePlotDf(geneAgeDf)
geneAgeText <- 1
p <- createGeneAgePlot(plotDf, geneAgeText)
expect_true(nrow(p$data) == 1)
})
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