tests/testthat/no_test/test_fetch_bam.R

In jrboyd/seqtsne: Application of t-sne to NGS Genomic Signal Profiles

testthat::context("Bam files")

library(data.table)
library(chiptsne)
library(testthat)

data("query_gr")

options("mc.cores" = 2)

bam_files = dir(system.file('extdata', package = "chiptsne"), pattern = ".bam$", full.names = TRUE)
cfg_dt = data.table(file = bam_files)
cfg_dt[, c("tall_var", "wide_var") := tstrsplit(basename(file), "_", keep = 1:2)]
cfg_dt = cfg_dt[tall_var %in% c("ESH1", "HUES48", "HUES64")]
cfg_dt[, norm_factor := ifelse(wide_var == "H3K4me3", .3, 1)]

# debug(seqsetvis::ssvFetchBam)
# debug(prep_profile_dt)
tsne_input = stsFetchTsneInput(cfg_dt, query_gr, force_overwrite = TRUE)


test_that("stsFetchTsneInput dimensions of outputs", {
    expect_equal(names(tsne_input), c("bw_dt", "query_gr", "rname"))
    expect_equal(nrow(tsne_input$bw_dt), length(query_gr)*nrow(cfg_dt)*50)
    # expect_equal(nrow(tsne_input$bw_mat), length(query_gr)*length(unique(cfg_dt$tall_var)))
    # expect_equal(ncol(tsne_input$bw_mat), length(unique(cfg_dt$wide_var))*50)
    expect_equal(length(tsne_input$query_gr), length(query_gr))
})

tsne_input$bw_dt$y = 0
# undebug(stsRunTsne)
test_that("stsRunTsne zero variance error", {
    expect_error({stsRunTsne(tsne_input$bw_dt,
                             perplexity = 15, force_overwrite = TRUE)},
                 regexp = "zero variance")
})

data("bam_pileup_dt")
tsne_input$bw_dt = bam_pileup_dt
tsne_input$bw_mat = chiptsne:::dt2mat(bam_pileup_dt, wide_vars = unique(bam_pileup_dt$wide_var))

tsne_res = stsRunTsne(tsne_input$bw_dt,
           perplexity = 15, force_overwrite = TRUE)

test_that("stsRunTsne dimensions of outputs", {
    expect_equal(colnames(tsne_res), c("tx", "ty", "id", "tall_var"))
    expect_equal(nrow(tsne_res), length(query_gr)*length(unique(cfg_dt$tall_var)))
})
#
#
# # #
# # # bw_dt = tsne_input$bw_dt
# # # setkey(bw_dt, id, tall_var, wide_var)
# # #
# # # np = 15
# # # img_res = make_tsne_img(tsne_input$bw_dt, tsne_res, np, odir = "~/tsne_images", force_rewrite = TRUE)
# # # p = plot_tsne_img(img_res$images_dt, np, min_size = .5, N_ceiling = 2)
# # # p$plot
# # #
# # # bw_dt[.(c("region_1", "region_2"), "ESH1")]
# # #
# # #
# # # plot_velocity_arrows(tsne_res, "ESH1", "HUES48", p = p$plot)[[1]]
# # #
# # # ggplot(tsne_res, aes(x = tx, y = ty)) + geom_point()
# # #
# # # tsne_res[, id_short := sub(".+_", "", id)]
# # # ggplot(tsne_res, aes(x = tx, y = ty, color = tall_var, label = id_short)) + geom_text()
# # # lab_dt = tsne_res[, .(tx = mean(tx), ty = mean(ty)), by = .(id_short)]
# # # ggplot(tsne_res, aes(x = tx, y = ty, group = id_short, label = id_short)) +
# # #     geom_polygon(color = "gray70", fill = "gray90") +
# # #     geom_text(data = lab_dt, color = "black", vjust = .5, hjust = .5) +
# # #     theme_classic()
# # #
# # #
# #
# #
# #