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REPRO-Bench / 101 /replication_package /plot_maps_main.R
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#plotting maps
source("set_up_inla.R")
metrics_joined <- metrics_joined %>%
filter(!is.na(L1_log10_st)) %>%
rename(L1_log_st = L1_log10_st) %>%
mutate(L1_copy = L1_log_st) %>%
filter(!is.na(L2_prop)) %>%
dplyr::mutate(L2_prop = scale(L2_prop)[, 1]) %>%
mutate(L2_copy = L2_prop) %>%
filter(!is.na(neighboring_languages_st)) %>%
filter(!is.na(Official)) %>%
filter(!is.na(Education)) %>%
filter(!is.na(boundness_st)) %>%
filter(!is.na(informativity_st))
#an overview of area and family coverage
tab_areas <- as.data.frame(table(metrics_joined$AUTOTYP_area)) %>%
arrange(desc(Freq))
tab_families <- as.data.frame(table(metrics_joined$Family_ID)) %>%
arrange(desc(Freq))
#dropping tips not in Grambank
metrics_joined <-
metrics_joined[metrics_joined$Language_ID %in% tree$tip.label,]
tree <- keep.tip(tree, metrics_joined$Language_ID)
x <-
assert_that(all(tree$tip.label %in% metrics_joined$Language_ID), msg = "The data and phylogeny taxa do not match")
world <-
map_data(
'world',
wrap = c(-25, 335),
ylim = c(-56, 80),
margin = T
)
lakes <-
map_data(
"lakes",
wrap = c(-25, 335),
col = "white",
border = "gray",
ylim = c(-55, 65),
margin = T
)
#shifting the longlat of the dataframe to match the pacific centered map
combination <- metrics_joined %>%
mutate(Longitude = if_else(Longitude <= -25, Longitude + 360, Longitude))
#duplicates?
combination %>%
group_by(Language_ID) %>%
mutate(dupe = n() > 1) -> combination_dup
dupes <- combination_dup[combination_dup$dupe == "TRUE", ]
#Basemap
basemap <- ggplot(combination) +
geom_polygon(
data = world,
aes(x = long, y = lat, group = group),
colour = "gray87",
fill = "gray87",
size = 0.5
) +
geom_polygon(
data = lakes,
aes(x = long, y = lat, group = group),
colour = "gray87",
fill = "white",
size = 0.3
) +
theme(
panel.grid.major = element_blank(),
#all of these lines are just removing default things like grid lines, axises etc
panel.grid.minor = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank(),
axis.line = element_blank(),
panel.border = element_blank(),
panel.background = element_rect(fill = "white"),
axis.text.x = element_blank(),
axis.text.y = element_blank(),
axis.ticks = element_blank()
) +
coord_map(projection = "vandergrinten", ylim = c(-56, 67))
#plotting informativity map
i <-
basemap + geom_point(
data = combination,
aes(x = Longitude, y = Latitude, colour = informativity_st, fill = informativity_st),
pch = 21,
size = 1.1,
alpha = 1,
position = position_jitter(
width = 1,
height = 1,
seed = 123
)
) +
scale_fill_viridis_c(option = "viridis", direction = -1) +
scale_color_viridis_c(option = "viridis",
guide = "none",
direction = -1) +
theme(
plot.title = element_text(size = 15),
legend.title = element_text(size = 15),
legend.text = element_text(size = 15),
legend.key.size = unit(0.5, units = "cm"),
legend.direction = "horizontal",
legend.position = c(.4, .07)
) +
guides(fill = guide_colourbar()) +
labs(title = "Informativity", fill = "score")
i
ggsave(
file = "output/map_informativity.svg",
plot = i,
width = 10,
height = 9,
dpi=300
)
ggsave(
file = "output/map_informativity.tiff",
plot = i,
width = 10,
height = 9,
dpi=600
)
#plotting boundness map
b <-
basemap + geom_point(
data = combination,
aes(x = Longitude, y = Latitude, colour = boundness_st, fill = boundness_st),
pch = 21,
size = 1.1,
alpha = 1,
position = position_jitter(
width = 1,
height = 1,
seed = 123
)
) +
scale_fill_viridis_c(option = "magma", direction = -1) +
scale_color_viridis_c(option = "magma",
guide = "none",
direction = -1) +
theme(
plot.title = element_text(size = 15),
legend.title = element_text(size = 15),
legend.text = element_text(size = 15),
legend.key.size = unit(0.5, units = "cm"),
legend.direction = "horizontal",
legend.position = c(.4, .07)
) +
guides(fill = guide_colourbar()) +
labs(title = "Boundness", fill = "score")
ggsave(
file = "output/map_boundness.svg",
plot = b,
width = 10,
height = 9,
dpi=300
)
ggsave(
file = "output/map_boundness.tiff",
plot = b,
width = 10,
height = 9,
dpi=600
)
i <-
basemap + geom_point(
data = combination,
aes(
x = Longitude,
y = Latitude,
fill = informativity_st,
color = informativity_st
),
pch = 21,
size = 1.1,
alpha = 1,
position = position_jitter(
width = 1,
height = 1,
seed = 123
)
) +
scale_fill_viridis_c(option = "viridis", direction = -1) +
scale_color_viridis_c(option = "viridis", direction = -1) +
theme(
text = element_text(size = 15),
legend.text = element_text(size = 15),
legend.key.size = unit(0.5, units = "cm"),
legend.direction = "horizontal",
legend.position = c(.4, .07)
) +
guides(fill = guide_colourbar(), color = "none") +
labs(fill = "informativity")
b <-
basemap + geom_point(
data = combination,
aes(
x = Longitude,
y = Latitude,
fill = boundness_st,
color = boundness_st
),
pch = 21,
size = 1.1,
alpha = 1,
position = position_jitter(
width = 1,
height = 1,
seed = 123
)
) +
scale_fill_viridis_c(option = "magma", direction = -1) +
scale_color_viridis_c(option = "magma", direction = -1) +
theme(
text = element_text(size = 15),
legend.text = element_text(size = 15),
legend.key.size = unit(0.5, units = "cm"),
legend.direction = "horizontal",
legend.position = c(.4, .07)
) +
guides(fill = guide_colourbar(), color = "none") +
labs(fill = "fusion")
two_maps <- b / i
ggsave(
file = "output/maps.tiff",
plot = two_maps,
width = 5,
height = 7,
dpi=800
)
ggsave(
file = "output/maps.svg",
plot = two_maps,
width = 5,
height = 7,
dpi=600
)
ggsave(
file = "output/maps.pdf",
plot = two_maps,
width = 5,
height = 7,
dpi=600
)
ggsave(
file = "output/maps.jpeg",
plot = two_maps,
width = 5,
height = 7,
dpi=600
)
#histograms
# hist_b <- ggplot(metrics_joined, aes(x = boundness_st)) +
# geom_histogram(color = "black", aes(fill = ..x..)) +
# scale_fill_viridis_c(option = "magma", direction = -1) +
# labs(x = "fusion", fill = "score") +
# theme_classic(base_size = 22)
#
# hist_i <- ggplot(metrics_joined, aes(x = informativity_st)) +
# geom_histogram(color = "black", aes(fill = ..x..)) +
# scale_fill_viridis_c(option = "viridis", direction = -1) +
# labs(x = "informativity", fill = "score") +
# theme_classic(base_size = 22)
#
# ggsave(
# file = "output/hist_boundness.svg",
# plot = hist_b,
# width = 7,
# height = 5,
# dpi=300
# )
# ggsave(
# file = "output/hist_informativity.svg",
# plot = hist_i,
# width = 7,
# height = 5,
# dpi=300
# )