Last updated: 2025-11-13
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Knit directory: PAINT/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 0236dab | Lily Heald | 2025-11-13 | log transformed depth |
| html | 08dda7e | Lily Heald | 2025-11-13 | update depth plot |
| Rmd | 1bfb83f | Lily Heald | 2025-11-13 | update map, axes |
| Rmd | a1afed5 | Lily Heald | 2025-11-07 | update visibility |
| html | a1afed5 | Lily Heald | 2025-11-07 | update visibility |
| html | 735357b | Lily Heald | 2025-11-07 | Build site. |
| Rmd | 50940c0 | Lily Heald | 2025-11-07 | Update introduction.Rmd |
| Rmd | f1b70cb | Lily Heald | 2025-11-07 | add Hstadel depth |
| Rmd | 7beeddd | Lily Heald | 2025-11-07 | add depth figure |
| Rmd | 967f438 | Lily Heald | 2025-11-07 | update callout |
| html | 967f438 | Lily Heald | 2025-11-07 | update callout |
| html | cc7d134 | Lily Heald | 2025-11-06 | updated figures |
| Rmd | b2f5585 | Lily Heald | 2025-11-06 | Update introduction.Rmd |
| html | 13755f1 | Lily Heald | 2025-11-06 | workflowr |
| Rmd | 46a0913 | Lily Heald | 2025-11-06 | start workflowr |
world <- ne_countries(scale = "medium", returnclass = "sf")
uv_matrix <- as.matrix(read.csv("data/neo_uvi.csv", header = F))
lon <- seq(-179.75, 179.75, by = 0.5)
lat <- seq(89.75, -89.75, by = -0.5)
rownames(uv_matrix) <- lat
colnames(uv_matrix) <- lon
uv_df <- melt(uv_matrix, varnames = c("lat", "lon"), value.name = "UVIndex")
uv_df$lat <- as.numeric(as.character(uv_df$lat))
uv_df$lon <- as.numeric(as.character(uv_df$lon))uv_raster <- rasterFromXYZ(uv_df[, c("lon", "lat", "UVIndex")], crs = "+proj=longlat +datum=WGS84")
world_sp <- as(world, "Spatial")
uv_land <- mask(uv_raster, world_sp)
uv_land_df <- as.data.frame(uv_land, xy = TRUE)
names(uv_land_df) <- c("lon", "lat", "UVIndex")sites <- data.frame(
name = c("Denisova","Chagyrskaya","Vindija", "Mezmaiskaya",
"El Sidron", "Spy","Les Cottés"),
samples = c("Denisova 3 (Denisovan)\nDenisova 11 (F1 Hybrid)\n Denisova 5 (Neanderthal)\n Denisova 25 (Denisovan)",
"Chagyrskaya 8 (Neanderthal)",
"Vindija 33.19 (Neanderthal)",
"Mezmaiskaya 1 (Neanderthal)\n Mezmaiskaya 2 (Neanderthal)",
"El Sidron",
"Spy 94-a",
"Les Cottés Z4-1415"),
lon = c(84.7, 83.1, 16.8, 40, -5.3, 4.7, 2.5), #E (+) W (-)
lat = c(51.4, 51.3, 46.3, 44.1, 43.4, 50.5, 46.2) #N (+) S (-)
)
sites_sf <- st_as_sf(sites, coords = c("lon","lat"), crs = 4326)Genome availability
wes_cols <- wes_palette("Zissou1", 100, type = "continuous")
ggplot() +
geom_raster(data = uv_land_df, aes(x = lon, y = lat, fill = UVIndex)) +
scale_fill_gradientn(colours = wes_cols, name = "UV Index", na.value = "white") +
geom_sf(data = world, fill = NA, color = "grey60", size = 0.2) +
geom_point(data = sites, aes(x = lon, y = lat),
color = "#00008B", fill = "#00008B", shape = 21, size = 3, stroke = 1) +
geom_label_repel(
data = sites,
aes(x = lon, y = lat, label = samples),
box.padding = 0.7,
point.padding = 0.3,
segment.color = "#00008B",
segment.size = 0.4,
fill = alpha("white", 0.8),
label.r = unit(0.2, "lines"),
color = "black",
size = 3,
label.size = 0.3,
family = "lato",
min.segment.length = 0
) +
coord_sf(expand = FALSE, xlim = c(-20, 150), ylim = c(20, 70)) +
theme_minimal(base_family = "lato") +
theme(
legend.position = c(0.9, 0.3),
legend.background = element_blank(),
panel.grid = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank(),
axis.title = element_blank(),
plot.title = element_text(size = 14, face = "bold", hjust = 0.5),
plot.subtitle = element_text(size = 10, hjust = 0.5)
) +
labs(
title = "Ancient DNA Discovery Sites and UV Radiation",
subtitle = "UV Index climatology (NASA AURA, 2010)"
)
Sequencing coverage
wes_samples <- wes_palette("Darjeeling1", 5, type = "discrete")
ggplot(depth_all, aes(x = Position, y = Depth, color = Sample)) +
geom_point(size = 2, alpha = 0.6) +
scale_color_manual(values = wes_samples) +
labs(
title = "Sequencing Depth",
subtitle = "EBI pigmentation-related loci",
x = "Genomic Position",
y = "Depth (coverage)",
color = "Sample"
) +
theme_bw(base_size = 14) +
theme_minimal(base_family = "lato") +
theme(
legend.position = "top",
legend.background = element_blank(),
panel.grid = element_blank(),
plot.title = element_text(size = 14, face = "bold", hjust = 0.5),
plot.subtitle = element_text(size = 10, hjust = 0.5)
)
wes_samples <- wes_palette("Darjeeling1", 5, type = "discrete")
ggplot(depth_all, aes(x = Position, y = log(Depth), color = Sample)) +
geom_point(size = 2, alpha = 0.6) +
scale_color_manual(values = wes_samples) +
labs(
title = "Sequencing Depth",
subtitle = "EBI pigmentation-related loci",
x = "Genomic Position",
y = "Depth (coverage)",
color = "Sample"
) +
theme_bw(base_size = 14) +
theme_minimal(base_family = "lato") +
theme(
legend.position = "top",
legend.background = element_blank(),
panel.grid = element_blank(),
axis.text.x = element_blank(),
plot.title = element_text(size = 14, face = "bold", hjust = 0.5),
plot.subtitle = element_text(size = 10, hjust = 0.5)
)
sessionInfo()R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Monterey 12.5.1
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
[4] sysfonts_0.8.9 reshape2_1.4.4 lubridate_1.9.4
[7] forcats_1.0.0 stringr_1.5.2 dplyr_1.1.4
[10] purrr_1.0.4 readr_2.1.5 tidyr_1.3.1
[13] tibble_3.3.0 tidyverse_2.0.0 ggrepel_0.9.6
[16] viridis_0.6.5 viridisLite_0.4.2 ggspatial_1.1.10
[19] raster_3.6-32 sp_2.2-0 sf_1.0-21
[22] rnaturalearthdata_1.0.0 rnaturalearth_1.1.0 ggplot2_4.0.0
[25] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] gtable_0.3.6 xfun_0.53 bslib_0.9.0 processx_3.8.6
[5] lattice_0.22-6 tzdb_0.5.0 callr_3.7.6 vctrs_0.6.5
[9] tools_4.4.2 ps_1.9.1 generics_0.1.4 curl_7.0.0
[13] proxy_0.4-27 pkgconfig_2.0.3 KernSmooth_2.23-26 RColorBrewer_1.1-3
[17] S7_0.2.0 lifecycle_1.0.4 compiler_4.4.2 farver_2.1.2
[21] git2r_0.35.0 terra_1.8-70 getPass_0.2-4 codetools_0.2-20
[25] httpuv_1.6.15 htmltools_0.5.8.1 class_7.3-23 sass_0.4.10
[29] yaml_2.3.10 later_1.4.4 pillar_1.11.1 jquerylib_0.1.4
[33] whisker_0.4.1 classInt_0.4-11 cachem_1.1.0 tidyselect_1.2.1
[37] digest_0.6.37 stringi_1.8.7 labeling_0.4.3 rprojroot_2.0.4
[41] fastmap_1.2.0 grid_4.4.2 cli_3.6.5 magrittr_2.0.4
[45] e1071_1.7-16 withr_3.0.2 scales_1.4.0 promises_1.3.3
[49] timechange_0.3.0 rmarkdown_2.29 httr_1.4.7 gridExtra_2.3
[53] hms_1.1.3 evaluate_1.0.5 knitr_1.50 rlang_1.1.6
[57] Rcpp_1.1.0 glue_1.8.0 DBI_1.2.3 rstudioapi_0.17.1
[61] jsonlite_2.0.0 plyr_1.8.9 R6_2.6.1 fs_1.6.6
[65] units_1.0-0