Nothing
# Test global reference filter
library(testthat)
library(SPUTNIK)
test_that("global reference filter", {
x <- bladderMALDIRompp2010(verbose = TRUE)
mz <- attr(x, "mass")
shape <- attr(x, "size")
msX <- msiDataset(values = x, mz = mz, rsize = shape[1], csize = shape[2])
msX <- normIntensity(msX, "median")
msX <- varTransform(msX, "log2")
refImg <- refImageContinuous(msX, method = "sum")
roiImg <- refImageBinaryOtsu(refImg)
cat("similarity: pearson
")
gpfPearson <- globalPeaksFilter(
msiData = msX, referenceImage = refImg,
method = "pearson", threshold = 0
)
cat("similarity: spearman
")
gpfSpearman <- globalPeaksFilter(
msiData = msX, referenceImage = refImg,
method = "spearman", threshold = 0
)
cat("similarity: ssim
")
gpfSSIM <- globalPeaksFilter(
msiData = msX, referenceImage = refImg,
method = "ssim",
threshold = 0
)
cat("similarity: nmi
")
gpfNMI <- globalPeaksFilter(
msiData = msX, referenceImage = roiImg,
method = "nmi", threshold = 0
)
expect_is(gpfPearson, "list")
expect_equal(attr(gpfPearson, "peak.filter"), T)
expect_equal(attr(gpfPearson, "filter"), "globalPeaks")
expect_is(gpfSpearman, "list")
expect_equal(attr(gpfSpearman, "peak.filter"), T)
expect_equal(attr(gpfSpearman, "filter"), "globalPeaks")
expect_is(gpfSSIM, "list")
expect_equal(attr(gpfSSIM, "peak.filter"), T)
expect_equal(attr(gpfSSIM, "filter"), "globalPeaks")
expect_is(gpfNMI, "list")
expect_equal(attr(gpfNMI, "peak.filter"), T)
expect_equal(attr(gpfNMI, "filter"), "globalPeaks")
expect_equal(length(gpfPearson$sel.peaks), 502)
expect_equal(length(gpfSpearman$sel.peaks), 586)
expect_equal(length(gpfSSIM$sel.peaks), 1125)
expect_equal(length(gpfNMI$sel.peaks), 515)
})
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