Small-sized Inversions - Inversion Simulations

Here, we visualize the inversions that were identified for the small treatment across the range of depths. The LEVIATHAN small, medium, and large call rates are configured to -s 95 -m 95 -l 90.

library(ggplot2)
options(warn = -1, repr.plot.width = 19, repr.plot.height = 10)
.size <- "small"

read_data <- function(size_treatment, depth){
    .depth <- paste("depth",depth, sep = "_")
    truthfile <- paste0("simulated_variants/inversions_genomes/", size_treatment, "/inv.", size_treatment,".vcf")
    samplesfile <- paste("simulated_data/called_sv/leviathan", size_treatment, .depth, "by_sample90/inversions.bedpe", sep = "/")
    poolfile <- paste("simulated_data/called_sv/leviathan", size_treatment, .depth, "by_pop90/inversions.bedpe", sep = "/")

    true_inversions <- read.table(truthfile, header = F)[,c(1,2,8)]
    true_inversions$V8 <- as.numeric(unlist(lapply(true_inversions$V8, function(X){gsub(".+END=", "", X)})))
    names(true_inversions) <- c("contig", "position_start", "position_end")
    true_inversions$sample <- "simulated_inversions"

    sample_inversions <- read.table(samplesfile, header = T)[,1:4]

    pooled_inversions <- read.table(poolfile, header = T)
    pooled_inversions <- pooled_inversions[,c("population","contig", "position_start", "position_end")]
    names(pooled_inversions)[1] <- "sample"
    if( nrow(pooled_inversions) > 0){
        pooled_inversions$sample <- paste("pooled", depth, size_treatment, sep = "_")
    }

    return(
        rbind(true_inversions, sample_inversions, pooled_inversions)
    )
}

plot_data <- function(data, size_treatment, depth){
    axis_ticks <- factor(c(paste("pooled", depth, size_treatment, sep = "_"), paste0("sample_", sprintf("%02d", 1:10)), "simulated_inversions"))
    ggplot(
        data,
        aes(
            x = position_start,
            xend = position_end,
            y = sample,
            yend = sample,
            color = sample
        )
    ) +
        scale_x_continuous(labels = scales::comma) +
        scale_y_discrete(limits = axis_ticks) +
        labs(title = "Called Inversions", subtitle = paste0("Size: ", size_treatment, " | Depth: ", depth,"X"), x = "genomic position (bp)", caption = "simulated_inversions are groundtruth") + 
        geom_segment(linewidth = 2) +
        facet_wrap(~contig, ncol = 1, scales = "free_x") +
        theme_light() +
        theme(panel.grid.major.y = element_blank(), legend.position = "None")
}

0.5X depth¶

depth_05X <- read_data(.size, 0.5)
tail(depth_05X)

plot_data(depth_05X, .size, 0.5)

2X Depth¶

depth_2X <- read_data(.size, 2)
tail(depth_2X)

plot_data(depth_2X, .size, 2)

5X Depth¶

depth_5X <- read_data(.size, 5)
tail(depth_5X)

plot_data(depth_5X, .size, 5)

10X Depth¶

depth_10X <- read_data(.size, 10)
tail(depth_10X)

plot_data(depth_10X, .size, 10)

20X Depth¶

depth_20X <- read_data(.size, 20)
tail(depth_20X)

plot_data(depth_20X, .size, 20)

Inversion Simulations

04 Check Called Inversions

LEVIATHAN

Medium-sized Inversions