Nothing
context("MANHATTAN")
test_that("snp_manhattan() works with unordered data", {
test <- snp_attachExtdata()
G <- test$genotypes
gwas <- big_univLogReg(G, test$fam$affection - 1L)
N <- ncol(G)
CHR <- sort(rep_len(1:2, N))
POS <- 1:N * 1000
rand <- sample(N)
# plot_grid(
# snp_manhattan(gwas, CHR, POS, dist.sep.chrs = 0),
# snp_manhattan(gwas[rand, ], CHR[rand], POS[rand], dist.sep.chrs = 0)
# )
expect_same_plot <- function(p1, p2) {
png1 <- ggplot2::ggsave(tempfile(fileext = ".png"), p1, width = 8, height = 6)
png2 <- ggplot2::ggsave(tempfile(fileext = ".png"), p2, width = 8, height = 6)
expect_identical(readBin(png1, what = raw(), n = 1e6),
readBin(png2, what = raw(), n = 1e6))
}
expect_failure(expect_same_plot(snp_manhattan(gwas, CHR, POS),
snp_manhattan(gwas, CHR, POS, npoints = 500)))
expect_same_plot(snp_manhattan(gwas, CHR, POS),
snp_manhattan(gwas[rand, ], CHR[rand], POS[rand]))
expect_same_plot(snp_manhattan(gwas, CHR, POS, npoints = 500),
snp_manhattan(gwas[rand, ], CHR[rand], POS[rand], npoints = 500))
expect_same_plot(snp_manhattan(gwas, as.character(CHR), POS, npoints = 500),
snp_manhattan(gwas[rand, ], as.character(CHR[rand]), POS[rand], npoints = 500))
})
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