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test_chromo_plot.R
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test_chromo_plot.R
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#
#
#library("testthat")
context("chromo_plot functions")
library(vcfR)
data("vcfR_example")
##### ##### ##### ##### #####
# chromo, vcf only
test_that("chromo works, variant data only",{
chrom <- create.chromR(name="Supercontig", vcf=vcf, verbose=FALSE)
chrom <- proc.chromR(chrom, verbose = FALSE)
expect_is(chrom, "chromR")
plot1 <- chromo( chrom, boxp = FALSE )
expect_true( is.null(plot1) )
plot2 <- chromo( chrom, boxp = TRUE )
expect_true( is.null(plot2) )
})
test_that("chromR plot when DP == NA",{
library(vcfR)
# trace('plot', browser, exit=browser, signature='chromR')
data(vcfR_test)
is.na(vcfR_test@fix[,'INFO']) <- TRUE
chrom <- create.chromR(vcfR_test, verbose = FALSE)
myPlot <- plot(chrom)
expect_true( is.null(myPlot) )
})
test_that("chromR plot when MQ == NA",{
library(vcfR)
# trace('plot', browser, exit=browser, signature='chromR')
data(vcfR_test)
is.na(vcfR_test@fix[,'INFO']) <- TRUE
chrom <- create.chromR(vcfR_test, verbose = FALSE)
myPlot <- plot(chrom)
expect_true( is.null(myPlot) )
})
##### ##### ##### ##### #####
# chromo, vcf and seq
test_that("chromo works, variant and seq data",{
chrom <- create.chromR(name="Supercontig", vcf=vcf, seq=dna, verbose=FALSE)
# chromo( chrom ) # Should error!
chrom <- proc.chromR(chrom, verbose = FALSE)
expect_is(chrom, "chromR")
plot1 <- chromo( chrom, boxp = FALSE )
expect_true( is.null(plot1) )
plot2 <- chromo( chrom, boxp = TRUE )
expect_true( is.null(plot2) )
})
##### ##### ##### ##### #####
# chromo, vcf and annotation
test_that("chromo works, variant and annotation data",{
chrom <- create.chromR(name="Supercontig", vcf=vcf, ann=gff, verbose=FALSE)
# chromo( chrom )
chrom <- proc.chromR(chrom, verbose = FALSE)
expect_is(chrom, "chromR")
plot1 <- chromo( chrom, boxp = FALSE )
expect_true( is.null(plot1) )
plot2 <- chromo( chrom, boxp = TRUE )
expect_true( is.null(plot2) )
})
##### ##### ##### ##### #####
# chromo, vcf, seq and annotation
test_that("chromo works, variant and annotation data",{
chrom <- create.chromR(name="Supercontig", vcf=vcf, seq=dna, ann=gff, verbose=FALSE)
# chromo( chrom )
chrom <- proc.chromR(chrom, verbose = FALSE)
expect_is(chrom, "chromR")
plot1 <- chromo( chrom, boxp = FALSE )
expect_true( is.null(plot1) )
plot2 <- chromo( chrom, boxp = TRUE )
expect_true( is.null(plot2) )
})
test_that("chromo works, vcf with no variants, seq or ann",{
data("vcfR_example")
vcf <- vcf[0,]
# chrom <- create.chromR(name="Supercontig", vcf=vcf, seq=dna, ann=gff, verbose=FALSE)
chrom <- create.chromR(name="Supercontig", vcf=vcf, verbose=FALSE)
# chrom@len
chrom <- proc.chromR(chrom, verbose = FALSE)
expect_is(chrom, 'chromR')
expect_equal( nrow(chrom@win.info), 0 )
})
test_that("chromo works, vcf with no variants",{
data("vcfR_example")
vcf <- vcf[0,]
chrom <- create.chromR(name="Supercontig", vcf=vcf, seq=dna, ann=gff, verbose=FALSE)
# chrom@len
chrom <- proc.chromR(chrom, verbose = FALSE)
expect_is(chrom, 'chromR')
expect_gt( nrow(chrom@win.info), 0 )
})
##### ##### ##### ##### #####
# chromo with custom tracks.
test_that("chromo works, custom tracks",{
chrom <- create.chromR(name="Supercontig", vcf=vcf, seq=dna, ann=gff, verbose=FALSE)
##### ##### ##### ##### #####
# Create lists of dots and rectangles
rlst1 <- cbind( gff[ seq(1,23, by=2) , 4 ],
0,
gff[ seq(1,23, by=2) , 5 ],
500
)
rlist <- list(rlst1)
myList1 <- list(title = "Track1",
dmat = chrom@var.info[,2:4],
rlst = rlst1,
rcol=4,
bwcol=1:2
)
##### ##### ##### ##### #####
# Custom plots.
plot1 <- chromo( chrom, boxp = FALSE, drlist1 = myList1 )
expect_true( is.null(plot1) )
chrom <- proc.chromR(chrom, verbose = FALSE)
plot2 <- chromo( chrom, boxp = FALSE , drlist1 = myList1 )
expect_true( is.null(plot2) )
plot3 <- chromo( chrom, boxp = TRUE , drlist1 = myList1 )
expect_true( is.null(plot3) )
plot4 <- chromo( chrom, boxp = TRUE , drlist1 = myList1, drlist2 = myList1 )
expect_true( is.null(plot4) )
plot5 <- chromo( chrom, boxp = TRUE , drlist1 = myList1, drlist2 = myList1, drlist3 = myList1 )
expect_true( is.null(plot5) )
})
# rlist, dcol, rcol, rbcol and bwcol.)
#names(myList1)
##### ##### ##### ##### #####
# Clean up when we're done.
unlink('Rplots.pdf')
# EOF.