tests/testthat/test_drplot.R

In vcfR: Manipulate and Visualize VCF Data

#library("testthat")
context("dr.plot functions")


library(vcfR)
data("vcfR_example")
#chrom <- create.chromR(name="Supercontig", vcf=vcf, verbose=FALSE)
#chrom <- create.chromR(name="Supercontig", vcf=vcf, seq=dna, verbose=FALSE)

chrom <- create.chromR(name="Supercontig", vcf=vcf, seq=dna, ann=gff, verbose=FALSE)
#chrom <- masker(chrom, min_QUAL=0, min_DP=350, max_DP=650, min_MQ=59.5, max_MQ=60.5)
chrom <- proc.chromR(chrom, verbose = FALSE)


##### ##### ##### ##### #####
# dr.plot

test_that("dr.plot creates a blank plot",{
  plot1 <- dr.plot( chrom.e = 100001 )
  expect_is(plot1, "numeric")
  expect_equal( length(plot1), 2)
})

#head(chrom@win.info)


##### ##### ##### ##### #####
# Create some data.

mat1 <- cbind(chrom@win.info[,'start'],
              0, 
              chrom@win.info[,'end'], 
              chrom@win.info[,'variants']
              )

mat2 <- cbind(chrom@win.info[,'start'],
              0, 
              chrom@win.info[,'end'],
              rowSums(chrom@win.info[,c('A', 'T')])
)

mat3 <- cbind(chrom@win.info[,'start'],
              rowSums(chrom@win.info[,c('A', 'T')]),
              chrom@win.info[,'end'],
              rowSums(chrom@win.info[,c('A', 'C', 'G', 'T')])
)

##### ##### ##### ##### #####


test_that("dr.plot creates a single barchart",{
  plot2 <- dr.plot( rlst = mat1, chrom.e = 100001 )
  expect_is(plot2, "numeric")
  expect_equal( length(plot2), 2)
})

test_that("dr.plot creates a stacked barchart",{
  plot3 <- dr.plot( rlst = list(mat2, mat3), chrom.e = 100001 )
  expect_is(plot3, "numeric")
  expect_equal( length(plot3), 2)
})

test_that("dr.plot creates a stacked barchart, no y-axis",{
  plot4 <- dr.plot( rlst = list(mat2, mat3), chrom.e = 100001, xaxt = "n", yaxt = "n") #, frame.plot = TRUE )
  expect_is(plot4, "numeric")
  expect_equal( length(plot4), 2)
})


test_that("dr.plot creates a dot plot",{
  plot5 <- dr.plot( dmat = as.matrix( chrom@var.info[,c(2,3)] ), 
                    chrom.e = 100001,
                    dcol=c(rgb(34,139,34, maxColorValue = 255), rgb(0,206,209, maxColorValue = 255))
                    )
  expect_is(plot5, "numeric")
  expect_equal( length(plot5), 2)
})


test_that("dr.plot creates a subset dot plot",{
  plot6 <- dr.plot( dmat = as.matrix( chrom@var.info[chrom@var.info[,3] > 59,c(2,3)] ), 
                    chrom.e = 100001, 
                    dcol=c(rgb(34,139,34, maxColorValue = 255), rgb(0,206,209, maxColorValue = 255)) 
                    )
  expect_is(plot6, "numeric")
  expect_equal( length(plot6), 2)
})


test_that("dr.plot creates a two level dot plot",{
  plot7 <- dr.plot( dmat = as.matrix( chrom@var.info[,c(2,3,4)] ), 
                    chrom.e = 100001,
                    dcol=c(rgb(34,139,34, maxColorValue = 255), rgb(0,206,209, maxColorValue = 255)) 
                    )
  expect_is(plot7, "numeric")
  expect_equal( length(plot7), 2)
})


test_that("dr.plot creates a bar and dot plot",{
  plot8 <- dr.plot( dmat = as.matrix( chrom@var.info[,c(2,3,4)] ),
                    rlst = list(mat2, mat3), 
                    chrom.e = 100001,
                    dcol=c(rgb(34,139,34, maxColorValue = 255), rgb(0,206,209, maxColorValue = 255)) 
                    )
  axis(side=1)
  expect_is(plot8, "numeric")
  expect_equal( length(plot8), 2)
})


test_that("dr.plot creates a bar and dot plot with annotations",{
  plot9 <- dr.plot( dmat = as.matrix( chrom@var.info[,c(2,3,4)] ),
                    rlst = list(mat2, mat3), 
                    chrom.e = 100001,
                    dcol=c(rgb(34,139,34,100, maxColorValue = 255), rgb(0,206,209,100, maxColorValue = 255)),
                    rbcol = c("#000000", "#000000"),
                    xlim=c(1e4,3e4), 
                    title="MyPlot",
                    hline = seq(0, 5e3, by=5e2)
                    )
  axis(side=1)
  expect_is(plot9, "numeric")
  expect_equal( length(plot9), 2)
})