Nothing
tests/testthat/test-Lolliplot-class.R
In GenVisR: Genomic Visualizations in R
# packges needed
library(ggplot2)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(BSgenome.Hsapiens.UCSC.hg38)
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
BSgenome <- BSgenome.Hsapiens.UCSC.hg38
# define the objects for testing
# note Lolliplot can run in two modes, we need to check both,
# we use the internal dataset PIK3CA for this
# mode 1, amino acid changes are not present
keep <- c("Chromosome", "Start_Position", "End_Position", "Reference_Allele",
"Tumor_Seq_Allele2", "Tumor_Sample_Barcode", "Gene", "Variant_Classification")
dfObject.mode1 <- PIK3CA[,keep]
colnames(dfObject.mode1) <- c("chromosome", "start", "stop", "reference", "variant",
"sample", "gene", "consequence")
# mode 2, amino acid changes are present
keep <- c("Chromosome", "Start_Position", "End_Position", "Reference_Allele",
"Tumor_Seq_Allele2", "Tumor_Sample_Barcode", "Gene", "Variant_Classification",
"Transcript_ID", "HGVSp")
dfObject.mode2 <- PIK3CA[,keep]
colnames(dfObject.mode2) <- c("chromosome", "start", "stop", "reference", "variant",
"sample", "gene", "consequence", "transcript", "proteinCoord")
################################################################################
###### Test LolliplotData class and associated functions in constructor ########
################################################################################
context("LolliplotData Constructor")
###################### test toLolliplot ########################################
# Lolliplot can run in two modes depending on columns detected, test both
toLolliplot.mode1.out <- toLolliplot(dfObject.mode1, verbose=FALSE)
toLolliplot.mode2.out <- toLolliplot(dfObject.mode2, verbose=FALSE)
test_that("toLolliplot stops if a required column is not detected", {
dfObject.mode1$sample <- NULL
expect_error(toLolliplot(dfObject.mode1, verbose=FALSE))
})
test_that("toLolliplot works in verbose mode",{
expect_message(toLolliplot(dfObject.mode1, verbose=TRUE))
})
##################### test retriveMart #########################################
# make sure there's an internet connection, if not skip tests
biomart_success <- try(biomaRt::useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org"))
biomart_success <- !class(biomart_success) == "try-error"
if(biomart_success){
retrieveMart.out <- retrieveMart("hsapiens", host="www.ensembl.org", verbose=FALSE)
}
test_that("retrieveMart retrieves a valid mart for a given species", {
skip_if_not(biomart_success, "mart recieved try-error, biomart is possibly down or there is no internet connection.")
expect_true(class(retrieveMart.out) == "Mart")
})
test_that("retrieveMart errors if the species matches more than one dataset in the mart", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_error(retrieveMart("m", host="www.ensembl.org", verbose=FALSE))
})
test_that("retreiveMart errors if the supplied species is not found", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_error(retrieveMart("titan", host="www.ensembl.org", verbose=FALSE))
})
test_that("retreiveMart works in verbose mode", {
expect_message(retrieveMart("hsapiens", host="www.ensembl.org", verbose=TRUE))
})
############### test annotateGene ##############################################
if(biomart_success){
annotateGene.mode1.out <- annotateGene(toLolliplot.mode1.out,
transcript="ENST00000263967",
ensembl_mart=retrieveMart.out,
verbose=FALSE)
annotateGene.mode2.out <- annotateGene(toLolliplot.mode2.out,
transcript="ENST00000263967",
ensembl_mart=retrieveMart.out,
verbose=FALSE)
}
test_that("annotateGene adds the ensembl, hgnc, and entrez gene identifiers for the supplied transcript", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_equivalent(as.character(unique(annotateGene.mode1.out$biomaRt_ensembl_gene_id)), "ENSG00000121879")
expect_equivalent(as.character(unique(annotateGene.mode1.out$biomaRt_hgnc_symbol)), "PIK3CA")
expect_equivalent(as.character(unique(annotateGene.mode1.out$biomaRt_entrez_gene_id)), "5290")
})
test_that("annotateGene errors if no transcript is supplied", {
expect_error(annotateGene(toLolliplot.mode1.out,
transcript=NULL,
ensembl_mart=retrieveMart.out,
verbose=FALSE))
})
test_that("annotateGene warns if transcript is not a character", {
expect_warning(annotateGene(toLolliplot.mode1.out,
transcript=factor("ENST00000263967"),
ensembl_mart=retrieveMart.out,
verbose=FALSE))
})
test_that("annotateGene warns if more than 1 element is supplied to transcript", {
expect_warning(annotateGene(toLolliplot.mode1.out,
transcript=rep("ENST00000263967", 2),
ensembl_mart=retrieveMart.out,
verbose=FALSE))
})
test_that("annotateGene errors if a valid ensembl transcript is not supplied", {
expect_error(annotateGene(toLolliplot.mode1.out,
transcript="unicorn",
ensembl_mart=retrieveMart.out,
verbose=FALSE))
})
test_that("annotateGene works in verbose mode", {
expect_message(annotateGene(toLolliplot.mode1.out,
transcript="ENST00000263967",
ensembl_mart=retrieveMart.out,
verbose=TRUE))
})
################ test filterByGene #############################################
if(biomart_success){
filterByGene.mode1.out <- filterByGene(annotateGene.mode1.out, verbose=FALSE)
filterByGene.mode2.out <- filterByGene(annotateGene.mode2.out, verbose=FALSE)
}
test_that("filterByGene correctly filters data by gene", {
skip_if_not(biomart_success, "mart recieved try-error")
annotateGene.mode1.out$gene <- as.character(annotateGene.mode1.out$gene)
annotateGene.mode1.out$gene[1:length(annotateGene.mode1.out$gene)-1] <- c("newTranscript")
filterByGene.mode1.out <- filterByGene(annotateGene.mode1.out, verbose=FALSE)
expect_equal(nrow(filterByGene.mode1.out), 1)
})
test_that("filterByGene can determine which value to filter by", {
skip_if_not(biomart_success, "mart recieved try-error")
annotateGene.mode1.out$gene <- as.character(annotateGene.mode1.out$gene)
annotateGene.mode1.out$gene[1] <- as.character("PIK3CA")
annotateGene.mode1.out$gene[2:nrow(annotateGene.mode1.out)] <- as.character("unicorn")
filterByGene.mode1.out <- filterByGene(annotateGene.mode1.out, verbose=FALSE)
expect_equal(nrow(filterByGene.mode1.out), 1)
annotateGene.mode1.out$gene[1] <- as.character("5290")
annotateGene.mode1.out$gene[2:nrow(annotateGene.mode1.out)] <- as.character("unicorn")
filterByGene.mode1.out <- filterByGene(annotateGene.mode1.out, verbose=FALSE)
expect_equal(nrow(filterByGene.mode1.out), 1)
annotateGene.mode1.out$gene[1] <- as.character("ENSG00000121879")
annotateGene.mode1.out$gene[2:nrow(annotateGene.mode1.out)] <- as.character("unicorn")
filterByGene.mode1.out <- filterByGene(annotateGene.mode1.out, verbose=FALSE)
expect_equal(nrow(filterByGene.mode1.out), 1)
})
test_that("filterByGene errors if no gene is found to filter on", {
skip_if_not(biomart_success, "mart recieved try-error")
annotateGene.mode1.out$gene <- as.character(annotateGene.mode1.out$gene)
annotateGene.mode1.out$gene[1:length(annotateGene.mode1.out$gene)] <- c("unicorn")
expect_error(filterByGene(annotateGene.mode1.out, verbose=FALSE))
})
test_that("filterByGene prints status messages", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(filterByGene(annotateGene.mode1.out, verbose=TRUE))
})
############### test annotateTranscript ########################################
if(biomart_success){
annotateTranscript.mode1.out <- annotateTranscript(filterByGene.mode1.out, ensembl=retrieveMart.out, verbose=FALSE)
annotateTranscript.mode2.out <- annotateTranscript(filterByGene.mode2.out, ensembl=retrieveMart.out, verbose=FALSE)
}
test_that("annotateTranscript annotates an ensembl transcript if none is present", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_true("biomaRt_ensembl_transcript_id" %in% colnames(annotateTranscript.mode1.out))
})
test_that("annotateTranscript does not attempt to annotate a transcript if one is already present", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_true("ensembl_transcript_id" %in% colnames(annotateTranscript.mode2.out))
})
test_that("annotateTranscript works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(annotateTranscript(filterByGene.mode1.out, ensembl=retrieveMart.out, verbose=TRUE))
expect_message(annotateTranscript(filterByGene.mode2.out, ensembl=retrieveMart.out, verbose=TRUE))
})
######################### test annotateProteinCoord ############################
if(biomart_success){
annotateProteinCoord.mode1.out <- suppressWarnings(annotateProteinCoord(annotateTranscript.mode1.out,
ensembl=retrieveMart.out,
txdb=txdb,
BSgenome=BSgenome,
verbose=FALSE))
annotateProteinCoord.mode2.out <- suppressWarnings(annotateProteinCoord(annotateTranscript.mode2.out,
ensembl=retrieveMart.out,
txdb=NULL,
BSgenome=NULL,
verbose=FALSE))
}
test_that("annotateProteinCoord adds protein coordinates if none are present", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_true(class(annotateProteinCoord.mode1.out$proteinCoord) == "integer")
# check 1 position of what the annotation file said to what genvisr said
expect <- unique(annotateProteinCoord.mode2.out[annotateProteinCoord.mode2.out$ensembl_transcript_id == "ENST00000263967" &
annotateProteinCoord.mode2.out$chromosome == "chr3" &
annotateProteinCoord.mode2.out$start == "179218294" &
annotateProteinCoord.mode2.out$stop == "179218294",]$proteinCoord)
actual <- unique(annotateProteinCoord.mode1.out[annotateProteinCoord.mode1.out$ensembl_transcript_id == "ENST00000263967" &
annotateProteinCoord.mode1.out$chromosome == "chr3" &
annotateProteinCoord.mode1.out$start == "179218294" &
annotateProteinCoord.mode1.out$stop == "179218294",]$proteinCoord)
expect_equivalent(expect, actual)
})
test_that("annotateProteinCoord removes p. notation from protein coords if they are present", {
skip_if_not(biomart_success, "mart recieved try-error")
annotateTranscript.mode2.out <- annotateTranscript.mode2.out[1:5,]
annotateProteinCoord.mode2.out <- suppressWarnings(annotateProteinCoord(annotateTranscript.mode2.out,
ensembl=retrieveMart.out,
txdb=NULL,
BSgenome=NULL,
verbose=FALSE))
expect_true(is.numeric(annotateProteinCoord.mode1.out$proteinCoord))
})
test_that("annotateProteinCoord works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(suppressWarnings(annotateProteinCoord(annotateTranscript.mode1.out,
ensembl=retrieveMart.out,
txdb=txdb,
BSgenome=BSgenome,
verbose=TRUE)))
expect_message(suppressWarnings(annotateProteinCoord(annotateTranscript.mode2.out,
ensembl=retrieveMart.out,
txdb=txdb,
BSgenome=BSgenome,
verbose=TRUE)))
})
##################### test filterByTranscript ##################################
if(biomart_success){
filterByTranscript.mode1.out <- filterByTranscript(annotateProteinCoord.mode1.out,
transcript="ENST00000263967",
verbose=FALSE)
filterByTranscript.mode2.out <- filterByTranscript(annotateProteinCoord.mode2.out,
transcript="ENST00000263967",
verbose=FALSE)
}
test_that("filterByTranscript leaves only one transcript", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_equal(length(unique(filterByTranscript.mode1.out$ensembl_transcript_id)), 1)
expect_equal(length(unique(filterByTranscript.mode2.out$ensembl_transcript_id)), 1)
})
test_that("filterByTranscript will choose a transcript if none is provided", {
skip_if_not(biomart_success, "mart recieved try-error")
filterByTranscript.mode1.out <- filterByTranscript(annotateProteinCoord.mode1.out,
transcript=NULL,
verbose=FALSE)
filterByTranscript.mode2.out <- filterByTranscript(annotateProteinCoord.mode2.out,
transcript=NULL,
verbose=FALSE)
expect_equal(length(unique(filterByTranscript.mode1.out$ensembl_transcript_id)), 1)
expect_equal(length(unique(filterByTranscript.mode2.out$ensembl_transcript_id)), 1)
})
test_that("filterByTranscript warns of transcript input is not a character vector", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_warning(filterByTranscript(annotateProteinCoord.mode1.out,
transcript=factor("ENST00000263967"),
verbose=FALSE))
})
test_that("filterByTranscript warns if transcript input has multiple elements", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_warning(filterByTranscript(annotateProteinCoord.mode1.out,
transcript=rep("ENST00000263967", 2),
verbose=FALSE))
})
test_that("filterByTranscript warns if a given transcript is not found", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_warning(filterByTranscript(annotateProteinCoord.mode1.out,
transcript="unicorn",
verbose=FALSE), "Did not find")
})
test_that("filterByTranscript works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(filterByTranscript(annotateProteinCoord.mode1.out,
transcript="ENST00000263967",
verbose=TRUE))
expect_message(filterByTranscript(annotateProteinCoord.mode1.out,
transcript=NULL,
verbose=TRUE))
})
################ test calcMutFreq ##############################################
if(biomart_success){
calcMutFreq.mode1.out <- calcMutFreq(filterByTranscript.mode1.out,
verbose=FALSE)
calcMutFreq.mode2.out <- calcMutFreq(filterByTranscript.mode2.out,
verbose=FALSE)
}
test_that("calcMutFreq correctly calculates the mutation frequency", {
skip_if_not(biomart_success, "mart recieved try-error")
expected <- 13
actual <- unique(calcMutFreq.mode1.out[calcMutFreq.mode1.out$chromosome == "chr3" &
calcMutFreq.mode1.out$start == 179234297 &
calcMutFreq.mode1.out$stop == 179234297 &
calcMutFreq.mode1.out$reference == "A" &
calcMutFreq.mode1.out$variant == "T",]$mutationFreq)
expect_equal(expected, actual)
expected <- 13
actual <- unique(calcMutFreq.mode2.out[calcMutFreq.mode2.out$chromosome == "chr3" &
calcMutFreq.mode2.out$start == 179234297 &
calcMutFreq.mode2.out$stop == 179234297 &
calcMutFreq.mode2.out$reference == "A" &
calcMutFreq.mode2.out$variant == "T",]$mutationFreq)
expect_equal(expected, actual)
})
test_that("calcMutFreq works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(calcMutFreq(filterByTranscript.mode1.out,
verbose=TRUE))
})
################# test constructTranscriptData fetches domains #################
if(biomart_success){
constructTranscriptData.mode1.out <- constructTranscriptData(calcMutFreq.mode1.out,
ensembl_mart=retrieveMart.out,
verbose=FALSE)
constructTranscriptData.mode2.out <- constructTranscriptData(calcMutFreq.mode2.out,
ensembl_mart=retrieveMart.out,
verbose=FALSE)
}
test_that("constructTranscriptData is able to retrieve protein domains", {
skip_if_not(biomart_success, "mart recieved try-error")
constructTranscriptData.mode1.out <- constructTranscriptData.mode1.out[constructTranscriptData.mode1.out$source == "domain",]
expect_true(length(constructTranscriptData.mode1.out) >= 1)
constructTranscriptData.mode2.out <- constructTranscriptData.mode2.out[constructTranscriptData.mode2.out$source == "domain",]
expect_true(length(constructTranscriptData.mode2.out) >= 1)
})
test_that("constructTranscriptData is able to retrieve a protein length", {
skip_if_not(biomart_success, "mart recieved try-error")
constructTranscriptData.mode1.out <- constructTranscriptData.mode1.out[constructTranscriptData.mode1.out$source == "protein",]
expect_true(constructTranscriptData.mode1.out$proteinStop >= 1)
constructTranscriptData.mode2.out <- constructTranscriptData.mode2.out[constructTranscriptData.mode2.out$source == "protein",]
expect_true(constructTranscriptData.mode2.out$proteinStop >= 1)
})
test_that("constructTranscriptData stops if more than one transcript is detected", {
skip_if_not(biomart_success, "mart recieved try-error")
calcMutFreq.mode1.out[1, "ensembl_transcript_id"] <- "ENST00000263968"
expect_error(constructTranscriptData(calcMutFreq.mode1.out,
ensembl_mart=retrieveMart.out,
verbose=FALSE))
})
test_that("contructTranscriptData works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(constructTranscriptData(calcMutFreq.mode1.out,
ensembl_mart=retrieveMart.out,
verbose=TRUE))
})
############### test setTierTwo ################################################
if(biomart_success){
setTierTwo.mode1.out <- setTierTwo(calcMutFreq.mode1.out, proteinData=constructTranscriptData.mode1.out,
emphasize=NULL, verbose=FALSE)
setTierTwo.mode2.out <- setTierTwo(calcMutFreq.mode2.out, proteinData=constructTranscriptData.mode2.out,
emphasize=NULL, verbose=FALSE)
}
test_that("setTierTwo does not extend coordinates outside the protein", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_true(max(setTierTwo.mode1.out$proteinCoordAdj) <= max(constructTranscriptData.mode1.out$proteinStop))
expect_true(min(setTierTwo.mode1.out$proteinCoordAdj) <= min(constructTranscriptData.mode1.out$proteinStop))
})
test_that("setTierTwo increases the height of each different mutation that resides on the same amino acid", {
skip_if_not(biomart_success, "mart recieved try-error")
setTierTwo.mode1.out <- unique(setTierTwo.mode1.out[setTierTwo.mode1.out$proteinCoord=="345",
c("chromosome", "start", "stop", "reference",
"variant", "height", "mutationFreq")])
setTierTwo.mode1.out <- setTierTwo.mode1.out[order(-setTierTwo.mode1.out$mutationFreq),]
expect_true(head(setTierTwo.mode1.out$height, 1) < tail(setTierTwo.mode1.out$height, 1))
})
test_that("setTierTwo emphasize parameter works", {
skip_if_not(biomart_success, "mart recieved try-error")
setTierTwo.mode1.out <- setTierTwo(calcMutFreq.mode1.out, proteinData=constructTranscriptData.mode1.out,
emphasize=c(70, 81), verbose=FALSE)
setTierTwo.mode1.out <- setTierTwo.mode1.out[setTierTwo.mode1.out$tier == "second",]
expect_true(nrow(setTierTwo.mode1.out) == 3)
})
test_that("setTierTwo works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(setTierTwo(calcMutFreq.mode1.out, proteinData=constructTranscriptData.mode1.out,
emphasize=NULL, verbose=TRUE))
})
################## test setTierOne #############################################
if(biomart_success){
setTierOne.mode1.out <- setTierOne(setTierTwo.mode1.out, verbose=FALSE)
setTierOne.mode2.out <- setTierOne(setTierTwo.mode2.out, verbose=FALSE)
}
test_that("first tier mutation heights increase as the mutation frequency increases", {
skip_if_not(biomart_success, "mart recieved try-error")
setTierOne.mode1.out <- setTierOne.mode1.out[setTierOne.mode1.out$tier == "first",]
setTierOne.mode1.out <- setTierOne.mode1.out[order(setTierOne.mode1.out$mutationFreq),]
expect_true(all(diff(setTierOne.mode1.out$height) >= 0))
setTierOne.mode2.out <- setTierOne.mode2.out[setTierOne.mode2.out$tier == "first",]
setTierOne.mode2.out <- setTierOne.mode2.out[order(setTierOne.mode2.out$mutationFreq),]
expect_true(all(diff(setTierOne.mode2.out$height) >= 0))
})
test_that("setTierOne works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(setTierOne(setTierTwo.mode1.out, verbose=TRUE))
})
###################### test addLabel ###########################################
if(biomart_success){
addLabel.mode1.out <- addLabel(setTierOne.mode1.out, verbose=FALSE)
addLabel.mode2.out <- addLabel(setTierOne.mode2.out, verbose=FALSE)
}
test_that("addLabel adds only 1 label for each x/y coordinate", {
skip_if_not(biomart_success, "mart recieved try-error")
addLabel.mode1.out <- addLabel.mode1.out[addLabel.mode1.out$proteinCoordAdj == 118,]
actual <- sum(is.na(addLabel.mode1.out$label))
expected <- 4
expect_equivalent(expected, actual)
})
test_that("addLabel is able to correctly add labels in the expected format", {
skip_if_not(biomart_success, "mart recieved try-error")
expected <- "p.Phe83Ser"
actual <- as.character(addLabel.mode2.out[addLabel.mode2.out$proteinCoordAdj == 83]$label)
expect_equivalent(expected, actual)
expected <- "p.F83S"
actual <- as.character(addLabel.mode1.out[addLabel.mode1.out$proteinCoordAdj == 83]$label)
expect_equivalent(expected, actual)
})
test_that("addLabel works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(addLabel(setTierOne.mode1.out, verbose=TRUE))
})
###################### test setDomainHeights ###################################
if(biomart_success){
setDomainHeights.mode1.out <- setDomainHeights(constructTranscriptData.mode1.out, verbose=FALSE)
setDomainHeights.mode2.out <- setDomainHeights(constructTranscriptData.mode2.out, verbose=FALSE)
}
test_that("setDomainHeights domains are nested correctly", {
skip_if_not(biomart_success, "mart recieved try-error")
expected <- 7
actual <- setDomainHeights.mode1.out[setDomainHeights.mode1.out$interproShortDesc == "PI3/4_kinase_cat_sf",]$nest
expect_equivalent(expected, actual)
expected <- 3
actual <- setDomainHeights.mode1.out[setDomainHeights.mode1.out$interproShortDesc == "Ubiquitin-like_domsf",]$nest
expect_equivalent(expected, actual)
})
test_that("setDomainHeights adjusts heights correctly based on the nest value", {
skip_if_not(biomart_success, "mart recieved try-error")
setDomainHeights.mode1.out <- setDomainHeights.mode1.out[order(setDomainHeights.mode1.out$nest),]
expect_true(all(diff(setDomainHeights.mode1.out$maxHeight) >= 0))
setDomainHeights.mode1.out <- setDomainHeights.mode1.out[order(setDomainHeights.mode1.out$nest),]
expect_true(all(diff(setDomainHeights.mode1.out$minHeight) <= 0))
})
test_that("setDomainHeights works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(setDomainHeights(constructTranscriptData.mode1.out, verbose=TRUE))
})
############ test Lolliplotdata constructor ####################################
if(biomart_success){
LolliplotData.mode1.out <- suppressWarnings(LolliplotData(dfObject.mode1, transcript="ENST00000263967",
species="hsapiens", host="www.ensembl.org",
txdb=txdb, BSgenome=BSgenome, emphasize=NULL,
verbose=FALSE))
LolliplotData.mode2.out <- suppressWarnings(LolliplotData(dfObject.mode2, transcript="ENST00000263967",
species="hsapiens", host="www.ensembl.org",
txdb=NULL, BSgenome=NULL, emphasize=NULL,
verbose=FALSE))
}
test_that("LolliplotData outputs a S4 class object", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_s4_class(LolliplotData.mode1.out, "LolliplotData")
expect_s4_class(LolliplotData.mode2.out, "LolliplotData")
})
################################################################################
###### test the LolliplotPlots class and associated constructor functions ######
################################################################################
context("LolliplotPlots Constructor")
##################### test buildDensityPlot ####################################
test_that("buildDensityPlot constructs the expected plot", {
skip_on_bioc()
skip_on_travis()
skip_if_not(biomart_success, "mart recieved try-error")
buildDensityPlot.out <- buildDensityPlot(LolliplotData.mode1.out, plotALayers=NULL, verbose=FALSE)
vdiffr::expect_doppelganger("Lolliplot Density Plot", grid::grid.draw(buildDensityPlot.out))
})
test_that("buildDensityPlot is able to add layers to the plot", {
skip_on_bioc()
skip_on_travis()
skip_if_not(biomart_success, "mart recieved try-error")
test_layer <- list(ggplot2::geom_text(aes(label="TEST LAYER", x=500, y=.025), colour="red", size=10))
buildDensityPlot.out <- buildDensityPlot(LolliplotData.mode1.out, plotALayers=test_layer, verbose=FALSE)
vdiffr::expect_doppelganger("Lolliplot Density Plot Layer", grid::grid.draw(buildDensityPlot.out))
})
test_that("buildDensityPlot works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(buildDensityPlot(LolliplotData.mode1.out, plotALayers=NULL, verbose=TRUE))
})
test_that("buildDensityPlot errors if plotALayers is not a list", {
skip_if_not(biomart_success, "mart recieved try-error")
test_layer <- ggplot2::geom_text(aes(label="TEST LAYER", x=500, y=.025), colour="red", size=10)
expect_error(buildDensityPlot(LolliplotData.mode1.out, plotALayers=test_layer, verbose=FALSE))
})
####################### test buildLolliplot ####################################
test_that("buildLolliplot constructs a plot", {
skip_on_bioc()
skip_on_travis()
skip_if_not(biomart_success, "mart recieved try-error")
buildLolliplot.out <- buildLolliplot(LolliplotData.mode1.out, labelAA=FALSE,
DomainPalette=NULL, MutationPalette=NULL,
plotBLayers=NULL, verbose=FALSE)
vdiffr::expect_doppelganger("Lolliplot Plot Base", grid::grid.draw(buildLolliplot.out))
})
test_that("buildLolliplot successfullly adds layers", {
skip_on_bioc()
skip_on_travis()
skip_if_not(biomart_success, "mart recieved try-error")
test_layer <- list(ggplot2::geom_text(aes(label="TEST LAYER", x=500, y=1), colour="red", size=10))
buildLolliplot.out <- buildLolliplot(LolliplotData.mode1.out, labelAA=FALSE,
DomainPalette=NULL, MutationPalette=NULL,
plotBLayers=test_layer, verbose=FALSE)
vdiffr::expect_doppelganger("Lolliplot Plot Base add layer", grid::grid.draw(buildLolliplot.out))
})
test_that("buildLolliplot successfullly adds labels", {
skip_on_bioc()
skip_on_travis()
skip_if_not(biomart_success, "mart recieved try-error")
buildLolliplot.out <- buildLolliplot(LolliplotData.mode1.out, labelAA=TRUE,
DomainPalette=NULL, MutationPalette=NULL,
plotBLayers=NULL, verbose=FALSE)
vdiffr::expect_doppelganger("Lolliplot Plot Base add labels", grid::grid.draw(buildLolliplot.out))
})
test_that("buildLolliplot successfullly changes colors for domains", {
skip_on_bioc()
skip_on_travis()
skip_if_not(biomart_success, "mart recieved try-error")
domain_palette <- c("blue", "red", "green", "yellow", "orange", "purple",
"indianred", "salmon", "plum", "thistle", "seagreen1",
"slateblue1", "slategrey")
buildLolliplot.out <- buildLolliplot(LolliplotData.mode1.out, labelAA=FALSE,
DomainPalette=domain_palette, MutationPalette=NULL,
plotBLayers=NULL, verbose=FALSE)
vdiffr::expect_doppelganger("Lolliplot Plot Base add domain palette", grid::grid.draw(buildLolliplot.out))
})
test_that("buildLolliplot successfullly changes colors for mutations", {
skip_on_bioc()
skip_on_travis()
skip_if_not(biomart_success, "mart recieved try-error")
mutation_palette <- c("blue", "red", "green", "yellow")
buildLolliplot.out <- buildLolliplot(LolliplotData.mode1.out, labelAA=FALSE,
DomainPalette=NULL, MutationPalette=mutation_palette,
plotBLayers=NULL, verbose=FALSE)
vdiffr::expect_doppelganger("Lolliplot Plot Base add mutation palette", grid::grid.draw(buildLolliplot.out))
})
test_that("buildLolliplot works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(buildLolliplot(LolliplotData.mode1.out, labelAA=FALSE,
DomainPalette=NULL, MutationPalette=NULL,
plotBLayers=NULL, verbose=TRUE))
})
test_that("buildLolliplot warns if not enough colors are supplied to DomainPalette", {
skip_if_not(biomart_success, "mart recieved try-error")
domain_palette <- c("blue", "red", "green")
expect_warning(buildLolliplot(LolliplotData.mode1.out, labelAA=FALSE,
DomainPalette=domain_palette, MutationPalette=NULL,
plotBLayers=NULL, verbose=FALSE))
})
test_that("buildLolliplot warns if not enough colors are supplied to MutationPalette", {
skip_if_not(biomart_success, "mart recieved try-error")
mutation_palette <- c("blue", "red")
expect_warning(buildLolliplot(LolliplotData.mode1.out, labelAA=FALSE,
DomainPalette=NULL, MutationPalette=mutation_palette,
plotBLayers=NULL, verbose=FALSE))
})
test_that("buildLolliplot errors if plotBLayers is not a list", {
skip_if_not(biomart_success, "mart recieved try-error")
test_layer <- ggplot2::geom_text(aes(label="TEST LAYER", x=500, y=1), colour="red", size=10)
expect_error(buildLolliplot(LolliplotData.mode1.out, labelAA=FALSE,
DomainPalette=NULL, MutationPalette=NULL,
plotBLayers=test_layer, verbose=FALSE))
})
###################### test LolliplotPlots constructor #########################
if(biomart_success){
LolliplotPlots.out <- LolliplotPlots(LolliplotData.mode1.out, labelAA=FALSE,
DomainPalette=NULL, MutationPalette=NULL,
plotALayers=NULL, plotBLayers=NULL, verbose=FALSE)
}
test_that("LolliplotPlots constructor outputs a s4 class object", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_s4_class(LolliplotPlots.out, "LolliplotPlots")
})
################################################################################
################## test Lolliplot constructor ##################################
context("Lolliplot Final Plot")
if(biomart_success){
arrangeLolliplotPlot.out <- arrangeLolliplotPlot(LolliplotPlots.out, sectionHeights=NULL, verbose=FALSE)
}
test_that("arrangeLolliplotPlot constructs a plot", {
skip_on_bioc()
skip_on_travis()
skip_if_not(biomart_success, "mart recieved try-error")
vdiffr::expect_doppelganger("Final Lolliplot Base", grid::grid.draw(arrangeLolliplotPlot.out))
})
test_that("arrangeLolliplotPlot alters section heights", {
skip_on_bioc()
skip_on_travis()
skip_if_not(biomart_success, "mart recieved try-error")
arrangeLolliplotPlot.out <- arrangeLolliplotPlot(LolliplotPlots.out, sectionHeights=c(.1, .9), verbose=FALSE)
vdiffr::expect_doppelganger("Final Lolliplot alter section height", grid::grid.draw(arrangeLolliplotPlot.out))
})
test_that("arrangeLolliplotPlot correctly warns if section heights does not match the number of plots", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_warning(arrangeLolliplotPlot(LolliplotPlots.out, sectionHeights=c(1), verbose=FALSE))
})
test_that("arrangeLolliplotPlot correctly warns if section heights is not numeric", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_warning(arrangeLolliplotPlot(LolliplotPlots.out, sectionHeights=c("A"), verbose=FALSE))
})
############################ test Lolliplot and accessors#######################
if(biomart_success){
Lolliplot.out <- suppressWarnings(Lolliplot(dfObject.mode1, transcript="ENST00000263967",
species="hsapiens", host="www.ensembl.org",
txdb=txdb, BSgenome=BSgenome, emphasize=NULL,
DomainPalette=NULL, MutationPalette=NULL,
labelAA=TRUE, plotALayers=NULL, plotBLayers=NULL,
sectionHeights=NULL, verbose=FALSE))
}
test_that("Lolliplot constructor outputs a S4 class object", {
expect_s4_class(Lolliplot.out, "Lolliplot")
})
################################ draw plot #####################################
context("Lolliplot accessors")
test_that("drawPlot constructs a Lolliplot", {
skip_on_bioc()
skip_on_travis()
skip_if_not(biomart_success, "mart recieved try-error")
vdiffr::expect_doppelganger("drawPlot Lolliplot", drawPlot(Lolliplot.out))
})
################################# getGrob ######################################
test_that("getGrob outputs error if index is out of bounds", {
expect_error(getGrob(Lolliplot.out, index=10))
})
test_that("getGrob successfully retrieves grob objects", {
expect_s3_class(getGrob(Lolliplot.out, index=1), "gtable")
expect_s3_class(getGrob(Lolliplot.out, index=2), "gtable")
expect_s3_class(getGrob(Lolliplot.out, index=3), "gtable")
})
################################ getData #######################################
test_that("getData outputs error if no name or index is given", {
expect_error(getData(Lolliplot.out))
})
test_that("getData outputs error if index exceeds the number of slots", {
expect_error(getData(Lolliplot.out, index=10))
})
test_that("getData outputs error if supplied name is not a valid slot name", {
expect_error(getData(Lolliplot.out, name="shouldNotexist"))
})
test_that("getData retrieves specified slot data correctly", {
expect_s3_class(getData(Lolliplot.out, index=1), "data.table")
expect_equivalent(getData(Lolliplot.out, name="primaryData"), getData(Lolliplot.out, index=1))
})
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# packges needed
library(ggplot2)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(BSgenome.Hsapiens.UCSC.hg38)
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
BSgenome <- BSgenome.Hsapiens.UCSC.hg38
# define the objects for testing
# note Lolliplot can run in two modes, we need to check both,
# we use the internal dataset PIK3CA for this
# mode 1, amino acid changes are not present
keep <- c("Chromosome", "Start_Position", "End_Position", "Reference_Allele",
"Tumor_Seq_Allele2", "Tumor_Sample_Barcode", "Gene", "Variant_Classification")
dfObject.mode1 <- PIK3CA[,keep]
colnames(dfObject.mode1) <- c("chromosome", "start", "stop", "reference", "variant",
"sample", "gene", "consequence")
# mode 2, amino acid changes are present
keep <- c("Chromosome", "Start_Position", "End_Position", "Reference_Allele",
"Tumor_Seq_Allele2", "Tumor_Sample_Barcode", "Gene", "Variant_Classification",
"Transcript_ID", "HGVSp")
dfObject.mode2 <- PIK3CA[,keep]
colnames(dfObject.mode2) <- c("chromosome", "start", "stop", "reference", "variant",
"sample", "gene", "consequence", "transcript", "proteinCoord")
################################################################################
###### Test LolliplotData class and associated functions in constructor ########
################################################################################
context("LolliplotData Constructor")
###################### test toLolliplot ########################################
# Lolliplot can run in two modes depending on columns detected, test both
toLolliplot.mode1.out <- toLolliplot(dfObject.mode1, verbose=FALSE)
toLolliplot.mode2.out <- toLolliplot(dfObject.mode2, verbose=FALSE)
test_that("toLolliplot stops if a required column is not detected", {
dfObject.mode1$sample <- NULL
expect_error(toLolliplot(dfObject.mode1, verbose=FALSE))
})
test_that("toLolliplot works in verbose mode",{
expect_message(toLolliplot(dfObject.mode1, verbose=TRUE))
})
##################### test retriveMart #########################################
# make sure there's an internet connection, if not skip tests
biomart_success <- try(biomaRt::useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org"))
biomart_success <- !class(biomart_success) == "try-error"
if(biomart_success){
retrieveMart.out <- retrieveMart("hsapiens", host="www.ensembl.org", verbose=FALSE)
}
test_that("retrieveMart retrieves a valid mart for a given species", {
skip_if_not(biomart_success, "mart recieved try-error, biomart is possibly down or there is no internet connection.")
expect_true(class(retrieveMart.out) == "Mart")
})
test_that("retrieveMart errors if the species matches more than one dataset in the mart", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_error(retrieveMart("m", host="www.ensembl.org", verbose=FALSE))
})
test_that("retreiveMart errors if the supplied species is not found", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_error(retrieveMart("titan", host="www.ensembl.org", verbose=FALSE))
})
test_that("retreiveMart works in verbose mode", {
expect_message(retrieveMart("hsapiens", host="www.ensembl.org", verbose=TRUE))
})
############### test annotateGene ##############################################
if(biomart_success){
annotateGene.mode1.out <- annotateGene(toLolliplot.mode1.out,
transcript="ENST00000263967",
ensembl_mart=retrieveMart.out,
verbose=FALSE)
annotateGene.mode2.out <- annotateGene(toLolliplot.mode2.out,
transcript="ENST00000263967",
ensembl_mart=retrieveMart.out,
verbose=FALSE)
}
test_that("annotateGene adds the ensembl, hgnc, and entrez gene identifiers for the supplied transcript", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_equivalent(as.character(unique(annotateGene.mode1.out$biomaRt_ensembl_gene_id)), "ENSG00000121879")
expect_equivalent(as.character(unique(annotateGene.mode1.out$biomaRt_hgnc_symbol)), "PIK3CA")
expect_equivalent(as.character(unique(annotateGene.mode1.out$biomaRt_entrez_gene_id)), "5290")
})
test_that("annotateGene errors if no transcript is supplied", {
expect_error(annotateGene(toLolliplot.mode1.out,
transcript=NULL,
ensembl_mart=retrieveMart.out,
verbose=FALSE))
})
test_that("annotateGene warns if transcript is not a character", {
expect_warning(annotateGene(toLolliplot.mode1.out,
transcript=factor("ENST00000263967"),
ensembl_mart=retrieveMart.out,
verbose=FALSE))
})
test_that("annotateGene warns if more than 1 element is supplied to transcript", {
expect_warning(annotateGene(toLolliplot.mode1.out,
transcript=rep("ENST00000263967", 2),
ensembl_mart=retrieveMart.out,
verbose=FALSE))
})
test_that("annotateGene errors if a valid ensembl transcript is not supplied", {
expect_error(annotateGene(toLolliplot.mode1.out,
transcript="unicorn",
ensembl_mart=retrieveMart.out,
verbose=FALSE))
})
test_that("annotateGene works in verbose mode", {
expect_message(annotateGene(toLolliplot.mode1.out,
transcript="ENST00000263967",
ensembl_mart=retrieveMart.out,
verbose=TRUE))
})
################ test filterByGene #############################################
if(biomart_success){
filterByGene.mode1.out <- filterByGene(annotateGene.mode1.out, verbose=FALSE)
filterByGene.mode2.out <- filterByGene(annotateGene.mode2.out, verbose=FALSE)
}
test_that("filterByGene correctly filters data by gene", {
skip_if_not(biomart_success, "mart recieved try-error")
annotateGene.mode1.out$gene <- as.character(annotateGene.mode1.out$gene)
annotateGene.mode1.out$gene[1:length(annotateGene.mode1.out$gene)-1] <- c("newTranscript")
filterByGene.mode1.out <- filterByGene(annotateGene.mode1.out, verbose=FALSE)
expect_equal(nrow(filterByGene.mode1.out), 1)
})
test_that("filterByGene can determine which value to filter by", {
skip_if_not(biomart_success, "mart recieved try-error")
annotateGene.mode1.out$gene <- as.character(annotateGene.mode1.out$gene)
annotateGene.mode1.out$gene[1] <- as.character("PIK3CA")
annotateGene.mode1.out$gene[2:nrow(annotateGene.mode1.out)] <- as.character("unicorn")
filterByGene.mode1.out <- filterByGene(annotateGene.mode1.out, verbose=FALSE)
expect_equal(nrow(filterByGene.mode1.out), 1)
annotateGene.mode1.out$gene[1] <- as.character("5290")
annotateGene.mode1.out$gene[2:nrow(annotateGene.mode1.out)] <- as.character("unicorn")
filterByGene.mode1.out <- filterByGene(annotateGene.mode1.out, verbose=FALSE)
expect_equal(nrow(filterByGene.mode1.out), 1)
annotateGene.mode1.out$gene[1] <- as.character("ENSG00000121879")
annotateGene.mode1.out$gene[2:nrow(annotateGene.mode1.out)] <- as.character("unicorn")
filterByGene.mode1.out <- filterByGene(annotateGene.mode1.out, verbose=FALSE)
expect_equal(nrow(filterByGene.mode1.out), 1)
})
test_that("filterByGene errors if no gene is found to filter on", {
skip_if_not(biomart_success, "mart recieved try-error")
annotateGene.mode1.out$gene <- as.character(annotateGene.mode1.out$gene)
annotateGene.mode1.out$gene[1:length(annotateGene.mode1.out$gene)] <- c("unicorn")
expect_error(filterByGene(annotateGene.mode1.out, verbose=FALSE))
})
test_that("filterByGene prints status messages", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(filterByGene(annotateGene.mode1.out, verbose=TRUE))
})
############### test annotateTranscript ########################################
if(biomart_success){
annotateTranscript.mode1.out <- annotateTranscript(filterByGene.mode1.out, ensembl=retrieveMart.out, verbose=FALSE)
annotateTranscript.mode2.out <- annotateTranscript(filterByGene.mode2.out, ensembl=retrieveMart.out, verbose=FALSE)
}
test_that("annotateTranscript annotates an ensembl transcript if none is present", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_true("biomaRt_ensembl_transcript_id" %in% colnames(annotateTranscript.mode1.out))
})
test_that("annotateTranscript does not attempt to annotate a transcript if one is already present", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_true("ensembl_transcript_id" %in% colnames(annotateTranscript.mode2.out))
})
test_that("annotateTranscript works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(annotateTranscript(filterByGene.mode1.out, ensembl=retrieveMart.out, verbose=TRUE))
expect_message(annotateTranscript(filterByGene.mode2.out, ensembl=retrieveMart.out, verbose=TRUE))
})
######################### test annotateProteinCoord ############################
if(biomart_success){
annotateProteinCoord.mode1.out <- suppressWarnings(annotateProteinCoord(annotateTranscript.mode1.out,
ensembl=retrieveMart.out,
txdb=txdb,
BSgenome=BSgenome,
verbose=FALSE))
annotateProteinCoord.mode2.out <- suppressWarnings(annotateProteinCoord(annotateTranscript.mode2.out,
ensembl=retrieveMart.out,
txdb=NULL,
BSgenome=NULL,
verbose=FALSE))
}
test_that("annotateProteinCoord adds protein coordinates if none are present", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_true(class(annotateProteinCoord.mode1.out$proteinCoord) == "integer")
# check 1 position of what the annotation file said to what genvisr said
expect <- unique(annotateProteinCoord.mode2.out[annotateProteinCoord.mode2.out$ensembl_transcript_id == "ENST00000263967" &
annotateProteinCoord.mode2.out$chromosome == "chr3" &
annotateProteinCoord.mode2.out$start == "179218294" &
annotateProteinCoord.mode2.out$stop == "179218294",]$proteinCoord)
actual <- unique(annotateProteinCoord.mode1.out[annotateProteinCoord.mode1.out$ensembl_transcript_id == "ENST00000263967" &
annotateProteinCoord.mode1.out$chromosome == "chr3" &
annotateProteinCoord.mode1.out$start == "179218294" &
annotateProteinCoord.mode1.out$stop == "179218294",]$proteinCoord)
expect_equivalent(expect, actual)
})
test_that("annotateProteinCoord removes p. notation from protein coords if they are present", {
skip_if_not(biomart_success, "mart recieved try-error")
annotateTranscript.mode2.out <- annotateTranscript.mode2.out[1:5,]
annotateProteinCoord.mode2.out <- suppressWarnings(annotateProteinCoord(annotateTranscript.mode2.out,
ensembl=retrieveMart.out,
txdb=NULL,
BSgenome=NULL,
verbose=FALSE))
expect_true(is.numeric(annotateProteinCoord.mode1.out$proteinCoord))
})
test_that("annotateProteinCoord works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(suppressWarnings(annotateProteinCoord(annotateTranscript.mode1.out,
ensembl=retrieveMart.out,
txdb=txdb,
BSgenome=BSgenome,
verbose=TRUE)))
expect_message(suppressWarnings(annotateProteinCoord(annotateTranscript.mode2.out,
ensembl=retrieveMart.out,
txdb=txdb,
BSgenome=BSgenome,
verbose=TRUE)))
})
##################### test filterByTranscript ##################################
if(biomart_success){
filterByTranscript.mode1.out <- filterByTranscript(annotateProteinCoord.mode1.out,
transcript="ENST00000263967",
verbose=FALSE)
filterByTranscript.mode2.out <- filterByTranscript(annotateProteinCoord.mode2.out,
transcript="ENST00000263967",
verbose=FALSE)
}
test_that("filterByTranscript leaves only one transcript", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_equal(length(unique(filterByTranscript.mode1.out$ensembl_transcript_id)), 1)
expect_equal(length(unique(filterByTranscript.mode2.out$ensembl_transcript_id)), 1)
})
test_that("filterByTranscript will choose a transcript if none is provided", {
skip_if_not(biomart_success, "mart recieved try-error")
filterByTranscript.mode1.out <- filterByTranscript(annotateProteinCoord.mode1.out,
transcript=NULL,
verbose=FALSE)
filterByTranscript.mode2.out <- filterByTranscript(annotateProteinCoord.mode2.out,
transcript=NULL,
verbose=FALSE)
expect_equal(length(unique(filterByTranscript.mode1.out$ensembl_transcript_id)), 1)
expect_equal(length(unique(filterByTranscript.mode2.out$ensembl_transcript_id)), 1)
})
test_that("filterByTranscript warns of transcript input is not a character vector", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_warning(filterByTranscript(annotateProteinCoord.mode1.out,
transcript=factor("ENST00000263967"),
verbose=FALSE))
})
test_that("filterByTranscript warns if transcript input has multiple elements", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_warning(filterByTranscript(annotateProteinCoord.mode1.out,
transcript=rep("ENST00000263967", 2),
verbose=FALSE))
})
test_that("filterByTranscript warns if a given transcript is not found", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_warning(filterByTranscript(annotateProteinCoord.mode1.out,
transcript="unicorn",
verbose=FALSE), "Did not find")
})
test_that("filterByTranscript works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(filterByTranscript(annotateProteinCoord.mode1.out,
transcript="ENST00000263967",
verbose=TRUE))
expect_message(filterByTranscript(annotateProteinCoord.mode1.out,
transcript=NULL,
verbose=TRUE))
})
################ test calcMutFreq ##############################################
if(biomart_success){
calcMutFreq.mode1.out <- calcMutFreq(filterByTranscript.mode1.out,
verbose=FALSE)
calcMutFreq.mode2.out <- calcMutFreq(filterByTranscript.mode2.out,
verbose=FALSE)
}
test_that("calcMutFreq correctly calculates the mutation frequency", {
skip_if_not(biomart_success, "mart recieved try-error")
expected <- 13
actual <- unique(calcMutFreq.mode1.out[calcMutFreq.mode1.out$chromosome == "chr3" &
calcMutFreq.mode1.out$start == 179234297 &
calcMutFreq.mode1.out$stop == 179234297 &
calcMutFreq.mode1.out$reference == "A" &
calcMutFreq.mode1.out$variant == "T",]$mutationFreq)
expect_equal(expected, actual)
expected <- 13
actual <- unique(calcMutFreq.mode2.out[calcMutFreq.mode2.out$chromosome == "chr3" &
calcMutFreq.mode2.out$start == 179234297 &
calcMutFreq.mode2.out$stop == 179234297 &
calcMutFreq.mode2.out$reference == "A" &
calcMutFreq.mode2.out$variant == "T",]$mutationFreq)
expect_equal(expected, actual)
})
test_that("calcMutFreq works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(calcMutFreq(filterByTranscript.mode1.out,
verbose=TRUE))
})
################# test constructTranscriptData fetches domains #################
if(biomart_success){
constructTranscriptData.mode1.out <- constructTranscriptData(calcMutFreq.mode1.out,
ensembl_mart=retrieveMart.out,
verbose=FALSE)
constructTranscriptData.mode2.out <- constructTranscriptData(calcMutFreq.mode2.out,
ensembl_mart=retrieveMart.out,
verbose=FALSE)
}
test_that("constructTranscriptData is able to retrieve protein domains", {
skip_if_not(biomart_success, "mart recieved try-error")
constructTranscriptData.mode1.out <- constructTranscriptData.mode1.out[constructTranscriptData.mode1.out$source == "domain",]
expect_true(length(constructTranscriptData.mode1.out) >= 1)
constructTranscriptData.mode2.out <- constructTranscriptData.mode2.out[constructTranscriptData.mode2.out$source == "domain",]
expect_true(length(constructTranscriptData.mode2.out) >= 1)
})
test_that("constructTranscriptData is able to retrieve a protein length", {
skip_if_not(biomart_success, "mart recieved try-error")
constructTranscriptData.mode1.out <- constructTranscriptData.mode1.out[constructTranscriptData.mode1.out$source == "protein",]
expect_true(constructTranscriptData.mode1.out$proteinStop >= 1)
constructTranscriptData.mode2.out <- constructTranscriptData.mode2.out[constructTranscriptData.mode2.out$source == "protein",]
expect_true(constructTranscriptData.mode2.out$proteinStop >= 1)
})
test_that("constructTranscriptData stops if more than one transcript is detected", {
skip_if_not(biomart_success, "mart recieved try-error")
calcMutFreq.mode1.out[1, "ensembl_transcript_id"] <- "ENST00000263968"
expect_error(constructTranscriptData(calcMutFreq.mode1.out,
ensembl_mart=retrieveMart.out,
verbose=FALSE))
})
test_that("contructTranscriptData works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(constructTranscriptData(calcMutFreq.mode1.out,
ensembl_mart=retrieveMart.out,
verbose=TRUE))
})
############### test setTierTwo ################################################
if(biomart_success){
setTierTwo.mode1.out <- setTierTwo(calcMutFreq.mode1.out, proteinData=constructTranscriptData.mode1.out,
emphasize=NULL, verbose=FALSE)
setTierTwo.mode2.out <- setTierTwo(calcMutFreq.mode2.out, proteinData=constructTranscriptData.mode2.out,
emphasize=NULL, verbose=FALSE)
}
test_that("setTierTwo does not extend coordinates outside the protein", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_true(max(setTierTwo.mode1.out$proteinCoordAdj) <= max(constructTranscriptData.mode1.out$proteinStop))
expect_true(min(setTierTwo.mode1.out$proteinCoordAdj) <= min(constructTranscriptData.mode1.out$proteinStop))
})
test_that("setTierTwo increases the height of each different mutation that resides on the same amino acid", {
skip_if_not(biomart_success, "mart recieved try-error")
setTierTwo.mode1.out <- unique(setTierTwo.mode1.out[setTierTwo.mode1.out$proteinCoord=="345",
c("chromosome", "start", "stop", "reference",
"variant", "height", "mutationFreq")])
setTierTwo.mode1.out <- setTierTwo.mode1.out[order(-setTierTwo.mode1.out$mutationFreq),]
expect_true(head(setTierTwo.mode1.out$height, 1) < tail(setTierTwo.mode1.out$height, 1))
})
test_that("setTierTwo emphasize parameter works", {
skip_if_not(biomart_success, "mart recieved try-error")
setTierTwo.mode1.out <- setTierTwo(calcMutFreq.mode1.out, proteinData=constructTranscriptData.mode1.out,
emphasize=c(70, 81), verbose=FALSE)
setTierTwo.mode1.out <- setTierTwo.mode1.out[setTierTwo.mode1.out$tier == "second",]
expect_true(nrow(setTierTwo.mode1.out) == 3)
})
test_that("setTierTwo works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(setTierTwo(calcMutFreq.mode1.out, proteinData=constructTranscriptData.mode1.out,
emphasize=NULL, verbose=TRUE))
})
################## test setTierOne #############################################
if(biomart_success){
setTierOne.mode1.out <- setTierOne(setTierTwo.mode1.out, verbose=FALSE)
setTierOne.mode2.out <- setTierOne(setTierTwo.mode2.out, verbose=FALSE)
}
test_that("first tier mutation heights increase as the mutation frequency increases", {
skip_if_not(biomart_success, "mart recieved try-error")
setTierOne.mode1.out <- setTierOne.mode1.out[setTierOne.mode1.out$tier == "first",]
setTierOne.mode1.out <- setTierOne.mode1.out[order(setTierOne.mode1.out$mutationFreq),]
expect_true(all(diff(setTierOne.mode1.out$height) >= 0))
setTierOne.mode2.out <- setTierOne.mode2.out[setTierOne.mode2.out$tier == "first",]
setTierOne.mode2.out <- setTierOne.mode2.out[order(setTierOne.mode2.out$mutationFreq),]
expect_true(all(diff(setTierOne.mode2.out$height) >= 0))
})
test_that("setTierOne works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(setTierOne(setTierTwo.mode1.out, verbose=TRUE))
})
###################### test addLabel ###########################################
if(biomart_success){
addLabel.mode1.out <- addLabel(setTierOne.mode1.out, verbose=FALSE)
addLabel.mode2.out <- addLabel(setTierOne.mode2.out, verbose=FALSE)
}
test_that("addLabel adds only 1 label for each x/y coordinate", {
skip_if_not(biomart_success, "mart recieved try-error")
addLabel.mode1.out <- addLabel.mode1.out[addLabel.mode1.out$proteinCoordAdj == 118,]
actual <- sum(is.na(addLabel.mode1.out$label))
expected <- 4
expect_equivalent(expected, actual)
})
test_that("addLabel is able to correctly add labels in the expected format", {
skip_if_not(biomart_success, "mart recieved try-error")
expected <- "p.Phe83Ser"
actual <- as.character(addLabel.mode2.out[addLabel.mode2.out$proteinCoordAdj == 83]$label)
expect_equivalent(expected, actual)
expected <- "p.F83S"
actual <- as.character(addLabel.mode1.out[addLabel.mode1.out$proteinCoordAdj == 83]$label)
expect_equivalent(expected, actual)
})
test_that("addLabel works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(addLabel(setTierOne.mode1.out, verbose=TRUE))
})
###################### test setDomainHeights ###################################
if(biomart_success){
setDomainHeights.mode1.out <- setDomainHeights(constructTranscriptData.mode1.out, verbose=FALSE)
setDomainHeights.mode2.out <- setDomainHeights(constructTranscriptData.mode2.out, verbose=FALSE)
}
test_that("setDomainHeights domains are nested correctly", {
skip_if_not(biomart_success, "mart recieved try-error")
expected <- 7
actual <- setDomainHeights.mode1.out[setDomainHeights.mode1.out$interproShortDesc == "PI3/4_kinase_cat_sf",]$nest
expect_equivalent(expected, actual)
expected <- 3
actual <- setDomainHeights.mode1.out[setDomainHeights.mode1.out$interproShortDesc == "Ubiquitin-like_domsf",]$nest
expect_equivalent(expected, actual)
})
test_that("setDomainHeights adjusts heights correctly based on the nest value", {
skip_if_not(biomart_success, "mart recieved try-error")
setDomainHeights.mode1.out <- setDomainHeights.mode1.out[order(setDomainHeights.mode1.out$nest),]
expect_true(all(diff(setDomainHeights.mode1.out$maxHeight) >= 0))
setDomainHeights.mode1.out <- setDomainHeights.mode1.out[order(setDomainHeights.mode1.out$nest),]
expect_true(all(diff(setDomainHeights.mode1.out$minHeight) <= 0))
})
test_that("setDomainHeights works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(setDomainHeights(constructTranscriptData.mode1.out, verbose=TRUE))
})
############ test Lolliplotdata constructor ####################################
if(biomart_success){
LolliplotData.mode1.out <- suppressWarnings(LolliplotData(dfObject.mode1, transcript="ENST00000263967",
species="hsapiens", host="www.ensembl.org",
txdb=txdb, BSgenome=BSgenome, emphasize=NULL,
verbose=FALSE))
LolliplotData.mode2.out <- suppressWarnings(LolliplotData(dfObject.mode2, transcript="ENST00000263967",
species="hsapiens", host="www.ensembl.org",
txdb=NULL, BSgenome=NULL, emphasize=NULL,
verbose=FALSE))
}
test_that("LolliplotData outputs a S4 class object", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_s4_class(LolliplotData.mode1.out, "LolliplotData")
expect_s4_class(LolliplotData.mode2.out, "LolliplotData")
})
################################################################################
###### test the LolliplotPlots class and associated constructor functions ######
################################################################################
context("LolliplotPlots Constructor")
##################### test buildDensityPlot ####################################
test_that("buildDensityPlot constructs the expected plot", {
skip_on_bioc()
skip_on_travis()
skip_if_not(biomart_success, "mart recieved try-error")
buildDensityPlot.out <- buildDensityPlot(LolliplotData.mode1.out, plotALayers=NULL, verbose=FALSE)
vdiffr::expect_doppelganger("Lolliplot Density Plot", grid::grid.draw(buildDensityPlot.out))
})
test_that("buildDensityPlot is able to add layers to the plot", {
skip_on_bioc()
skip_on_travis()
skip_if_not(biomart_success, "mart recieved try-error")
test_layer <- list(ggplot2::geom_text(aes(label="TEST LAYER", x=500, y=.025), colour="red", size=10))
buildDensityPlot.out <- buildDensityPlot(LolliplotData.mode1.out, plotALayers=test_layer, verbose=FALSE)
vdiffr::expect_doppelganger("Lolliplot Density Plot Layer", grid::grid.draw(buildDensityPlot.out))
})
test_that("buildDensityPlot works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(buildDensityPlot(LolliplotData.mode1.out, plotALayers=NULL, verbose=TRUE))
})
test_that("buildDensityPlot errors if plotALayers is not a list", {
skip_if_not(biomart_success, "mart recieved try-error")
test_layer <- ggplot2::geom_text(aes(label="TEST LAYER", x=500, y=.025), colour="red", size=10)
expect_error(buildDensityPlot(LolliplotData.mode1.out, plotALayers=test_layer, verbose=FALSE))
})
####################### test buildLolliplot ####################################
test_that("buildLolliplot constructs a plot", {
skip_on_bioc()
skip_on_travis()
skip_if_not(biomart_success, "mart recieved try-error")
buildLolliplot.out <- buildLolliplot(LolliplotData.mode1.out, labelAA=FALSE,
DomainPalette=NULL, MutationPalette=NULL,
plotBLayers=NULL, verbose=FALSE)
vdiffr::expect_doppelganger("Lolliplot Plot Base", grid::grid.draw(buildLolliplot.out))
})
test_that("buildLolliplot successfullly adds layers", {
skip_on_bioc()
skip_on_travis()
skip_if_not(biomart_success, "mart recieved try-error")
test_layer <- list(ggplot2::geom_text(aes(label="TEST LAYER", x=500, y=1), colour="red", size=10))
buildLolliplot.out <- buildLolliplot(LolliplotData.mode1.out, labelAA=FALSE,
DomainPalette=NULL, MutationPalette=NULL,
plotBLayers=test_layer, verbose=FALSE)
vdiffr::expect_doppelganger("Lolliplot Plot Base add layer", grid::grid.draw(buildLolliplot.out))
})
test_that("buildLolliplot successfullly adds labels", {
skip_on_bioc()
skip_on_travis()
skip_if_not(biomart_success, "mart recieved try-error")
buildLolliplot.out <- buildLolliplot(LolliplotData.mode1.out, labelAA=TRUE,
DomainPalette=NULL, MutationPalette=NULL,
plotBLayers=NULL, verbose=FALSE)
vdiffr::expect_doppelganger("Lolliplot Plot Base add labels", grid::grid.draw(buildLolliplot.out))
})
test_that("buildLolliplot successfullly changes colors for domains", {
skip_on_bioc()
skip_on_travis()
skip_if_not(biomart_success, "mart recieved try-error")
domain_palette <- c("blue", "red", "green", "yellow", "orange", "purple",
"indianred", "salmon", "plum", "thistle", "seagreen1",
"slateblue1", "slategrey")
buildLolliplot.out <- buildLolliplot(LolliplotData.mode1.out, labelAA=FALSE,
DomainPalette=domain_palette, MutationPalette=NULL,
plotBLayers=NULL, verbose=FALSE)
vdiffr::expect_doppelganger("Lolliplot Plot Base add domain palette", grid::grid.draw(buildLolliplot.out))
})
test_that("buildLolliplot successfullly changes colors for mutations", {
skip_on_bioc()
skip_on_travis()
skip_if_not(biomart_success, "mart recieved try-error")
mutation_palette <- c("blue", "red", "green", "yellow")
buildLolliplot.out <- buildLolliplot(LolliplotData.mode1.out, labelAA=FALSE,
DomainPalette=NULL, MutationPalette=mutation_palette,
plotBLayers=NULL, verbose=FALSE)
vdiffr::expect_doppelganger("Lolliplot Plot Base add mutation palette", grid::grid.draw(buildLolliplot.out))
})
test_that("buildLolliplot works in verbose mode", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_message(buildLolliplot(LolliplotData.mode1.out, labelAA=FALSE,
DomainPalette=NULL, MutationPalette=NULL,
plotBLayers=NULL, verbose=TRUE))
})
test_that("buildLolliplot warns if not enough colors are supplied to DomainPalette", {
skip_if_not(biomart_success, "mart recieved try-error")
domain_palette <- c("blue", "red", "green")
expect_warning(buildLolliplot(LolliplotData.mode1.out, labelAA=FALSE,
DomainPalette=domain_palette, MutationPalette=NULL,
plotBLayers=NULL, verbose=FALSE))
})
test_that("buildLolliplot warns if not enough colors are supplied to MutationPalette", {
skip_if_not(biomart_success, "mart recieved try-error")
mutation_palette <- c("blue", "red")
expect_warning(buildLolliplot(LolliplotData.mode1.out, labelAA=FALSE,
DomainPalette=NULL, MutationPalette=mutation_palette,
plotBLayers=NULL, verbose=FALSE))
})
test_that("buildLolliplot errors if plotBLayers is not a list", {
skip_if_not(biomart_success, "mart recieved try-error")
test_layer <- ggplot2::geom_text(aes(label="TEST LAYER", x=500, y=1), colour="red", size=10)
expect_error(buildLolliplot(LolliplotData.mode1.out, labelAA=FALSE,
DomainPalette=NULL, MutationPalette=NULL,
plotBLayers=test_layer, verbose=FALSE))
})
###################### test LolliplotPlots constructor #########################
if(biomart_success){
LolliplotPlots.out <- LolliplotPlots(LolliplotData.mode1.out, labelAA=FALSE,
DomainPalette=NULL, MutationPalette=NULL,
plotALayers=NULL, plotBLayers=NULL, verbose=FALSE)
}
test_that("LolliplotPlots constructor outputs a s4 class object", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_s4_class(LolliplotPlots.out, "LolliplotPlots")
})
################################################################################
################## test Lolliplot constructor ##################################
context("Lolliplot Final Plot")
if(biomart_success){
arrangeLolliplotPlot.out <- arrangeLolliplotPlot(LolliplotPlots.out, sectionHeights=NULL, verbose=FALSE)
}
test_that("arrangeLolliplotPlot constructs a plot", {
skip_on_bioc()
skip_on_travis()
skip_if_not(biomart_success, "mart recieved try-error")
vdiffr::expect_doppelganger("Final Lolliplot Base", grid::grid.draw(arrangeLolliplotPlot.out))
})
test_that("arrangeLolliplotPlot alters section heights", {
skip_on_bioc()
skip_on_travis()
skip_if_not(biomart_success, "mart recieved try-error")
arrangeLolliplotPlot.out <- arrangeLolliplotPlot(LolliplotPlots.out, sectionHeights=c(.1, .9), verbose=FALSE)
vdiffr::expect_doppelganger("Final Lolliplot alter section height", grid::grid.draw(arrangeLolliplotPlot.out))
})
test_that("arrangeLolliplotPlot correctly warns if section heights does not match the number of plots", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_warning(arrangeLolliplotPlot(LolliplotPlots.out, sectionHeights=c(1), verbose=FALSE))
})
test_that("arrangeLolliplotPlot correctly warns if section heights is not numeric", {
skip_if_not(biomart_success, "mart recieved try-error")
expect_warning(arrangeLolliplotPlot(LolliplotPlots.out, sectionHeights=c("A"), verbose=FALSE))
})
############################ test Lolliplot and accessors#######################
if(biomart_success){
Lolliplot.out <- suppressWarnings(Lolliplot(dfObject.mode1, transcript="ENST00000263967",
species="hsapiens", host="www.ensembl.org",
txdb=txdb, BSgenome=BSgenome, emphasize=NULL,
DomainPalette=NULL, MutationPalette=NULL,
labelAA=TRUE, plotALayers=NULL, plotBLayers=NULL,
sectionHeights=NULL, verbose=FALSE))
}
test_that("Lolliplot constructor outputs a S4 class object", {
expect_s4_class(Lolliplot.out, "Lolliplot")
})
################################ draw plot #####################################
context("Lolliplot accessors")
test_that("drawPlot constructs a Lolliplot", {
skip_on_bioc()
skip_on_travis()
skip_if_not(biomart_success, "mart recieved try-error")
vdiffr::expect_doppelganger("drawPlot Lolliplot", drawPlot(Lolliplot.out))
})
################################# getGrob ######################################
test_that("getGrob outputs error if index is out of bounds", {
expect_error(getGrob(Lolliplot.out, index=10))
})
test_that("getGrob successfully retrieves grob objects", {
expect_s3_class(getGrob(Lolliplot.out, index=1), "gtable")
expect_s3_class(getGrob(Lolliplot.out, index=2), "gtable")
expect_s3_class(getGrob(Lolliplot.out, index=3), "gtable")
})
################################ getData #######################################
test_that("getData outputs error if no name or index is given", {
expect_error(getData(Lolliplot.out))
})
test_that("getData outputs error if index exceeds the number of slots", {
expect_error(getData(Lolliplot.out, index=10))
})
test_that("getData outputs error if supplied name is not a valid slot name", {
expect_error(getData(Lolliplot.out, name="shouldNotexist"))
})
test_that("getData retrieves specified slot data correctly", {
expect_s3_class(getData(Lolliplot.out, index=1), "data.table")
expect_equivalent(getData(Lolliplot.out, name="primaryData"), getData(Lolliplot.out, index=1))
})
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