Depth
Last updated: 2026-03-26
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Knit directory: ~/Documents/GitHub/PAINT/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 2d31b45 | Lily Heald | 2026-03-26 | Build site. |
| Rmd | 05c4750 | Lily Heald | 2026-03-26 | stack snp distribution |
| html | 05c4750 | Lily Heald | 2026-03-26 | stack snp distribution |
Sequencing coverage
Sequencing read alignments were processed using samtools. The input BAM file was first indexed, then coordinate-sorted and re-indexed to ensure compatibility with downstream analyses. Read depth was calculated for archaic samples at the specified pigmentation-related SNP panel using samtools depth including sites with zero coverage.
| Version | Author | Date |
|---|---|---|
| 05c4750 | Lily Heald | 2026-03-26 |
| Version | Author | Date |
|---|---|---|
| 05c4750 | Lily Heald | 2026-03-26 |
Missingness
In order to examine patterns of missingness, I created a heatmap of where sequencing depth = 0.
depth_all <- depth_all %>%
mutate(
Position = as.factor(Position),
Depth = as.numeric(Depth),
Position_bin = round(Position / 500000),
Depth_NA = ifelse(Depth > 0, log(Depth), NA) # avoid -Inf
)Warning: There was 1 warning in `mutate()`.
ℹ In argument: `Position_bin = round(Position/5e+05)`.
Caused by warning in `Ops.factor()`:
! '/' not meaningful for factorsggplot(depth_all, aes(x = Position, y = Sample)) +
geom_raster(aes(fill = Depth_NA)) +
scale_fill_gradientn(
colors = wes_palette("Zissou1", 100, type = "continuous"),
na.value = "grey70",
name = "log(Depth)"
) +
theme_minimal(base_family = "lato") +
theme(
axis.text.x = element_blank(),
axis.text.y = element_text(size = 8),
panel.spacing = unit(0.5, "lines")
) 
| Version | Author | Date |
|---|---|---|
| 05c4750 | Lily Heald | 2026-03-26 |
Manhattan style plot
depth_all <- depth_all %>%
mutate(
Position = as.numeric(as.character(Position)),
Depth = as.numeric(as.character(Depth))
)
depth_all <- depth_all %>%
arrange(Chromosome, Position) %>%
group_by(Chromosome) %>%
mutate(chr_len = max(Position, na.rm = TRUE)) %>%
ungroup() %>%
mutate(
chr_offset = cumsum(lag(chr_len, default = 0)),
Position_cum = Position + chr_offset,
Depth_log = ifelse(Depth > 0, log10(Depth), NA)
)
ggplot(depth_all, aes(x = Position_cum, y = Depth_log, color = Chromosome)) +
geom_point(size = 0.8, alpha = 0.8) +
scale_color_manual(
values = rep(wes_palette("Zissou1", 5), length.out = length(unique(depth_all$Chromosome)))
) +
theme_minimal(base_family = "lato") +
labs(
x = "Genomic Position",
y = "log10(Depth)",
color = "Chromosome"
)Warning: Removed 1329 rows containing missing values or values outside the scale range
(`geom_point()`).
| Version | Author | Date |
|---|---|---|
| 05c4750 | Lily Heald | 2026-03-26 |
ggplot(depth_all, aes(x = Position_cum, y = Depth_log, color = Chromosome)) +
geom_point(size = 0.6) +
facet_wrap(~ Sample, ncol = 3) +
scale_color_manual(
values = rep(wes_palette("Zissou1", 5), length.out = length(unique(depth_all$Chromosome)))
) +
theme_minimal(base_family = "lato") +
theme(
legend.position = "none",
strip.text = element_text(face = "bold")
) +
labs(
x = "Genomic Position",
y = "log10(Depth)"
)Warning: Removed 1329 rows containing missing values or values outside the scale range
(`geom_point()`).
| Version | Author | Date |
|---|---|---|
| 05c4750 | Lily Heald | 2026-03-26 |
sessionInfo()R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS 26.3.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Detroit
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] wesanderson_0.3.7 showtext_0.9-7 showtextdb_3.0 sysfonts_0.8.9
[5] lubridate_1.9.4 forcats_1.0.1 stringr_1.6.0 dplyr_1.2.0
[9] purrr_1.2.1 readr_2.1.6 tidyr_1.3.2 tibble_3.3.1
[13] tidyverse_2.0.0 ggplot2_4.0.2 workflowr_1.7.2
loaded via a namespace (and not attached):
[1] sass_0.4.10 generics_0.1.4 stringi_1.8.7 hms_1.1.4
[5] digest_0.6.39 magrittr_2.0.4 timechange_0.4.0 evaluate_1.0.5
[9] grid_4.4.2 RColorBrewer_1.1-3 fastmap_1.2.0 rprojroot_2.1.1
[13] jsonlite_2.0.0 processx_3.8.6 whisker_0.4.1 ps_1.9.1
[17] promises_1.5.0 httr_1.4.7 scales_1.4.0 jquerylib_0.1.4
[21] cli_3.6.5 rlang_1.1.7 withr_3.0.2 cachem_1.1.0
[25] yaml_2.3.12 otel_0.2.0 tools_4.4.2 tzdb_0.5.0
[29] httpuv_1.6.16 curl_7.0.0 vctrs_0.7.1 R6_2.6.1
[33] lifecycle_1.0.5 git2r_0.36.2 fs_1.6.6 pkgconfig_2.0.3
[37] callr_3.7.6 pillar_1.11.1 bslib_0.10.0 later_1.4.5
[41] gtable_0.3.6 glue_1.8.0 Rcpp_1.1.1 xfun_0.56
[45] tidyselect_1.2.1 rstudioapi_0.18.0 knitr_1.51 farver_2.1.2
[49] htmltools_0.5.9 labeling_0.4.3 rmarkdown_2.30 compiler_4.4.2
[53] getPass_0.2-4 S7_0.2.1