File size: 2,956 Bytes
2f8aa81 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 | #heat map with a tree plot: boundness
#first, obtaining the actual max and min values of informativity in the entire sample
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))
#dropping tips not in Grambank
metrics_joined <-
metrics_joined[metrics_joined$Language_ID %in% tree$tip.label,]
max <- max(metrics_joined$informativity_st)
min <- min(metrics_joined$informativity_st)
#now plotting Uralic languages only
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)) %>%
filter(Family_ID == "ural1272")
#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")
metrics_joined <-
metrics_joined %>% mutate(Language_ID_2 = Language_ID) %>% column_to_rownames(var = "Language_ID_2")
df1 <- metrics_joined %>%
dplyr::select(informativity_st) %>%
rename(informativity = informativity_st)
uralic_fam_tree <-
ggtree(tree, layout = 'rect', branch.length = 'none')
uralic_fam_tree <-
uralic_fam_tree %<+% metrics_joined + geom_tiplab(aes(label = Name), size =
5)
p1 <-
gheatmap(
uralic_fam_tree,
df1,
offset = 6,
width = .2,
colnames_angle = 0,
colnames_position = "top",
colnames = F,
#removing column names
font.size = 5,
hjust = 0.5,
color = FALSE
) + #ylim(-5, 27) + #ylim(-5, 1450)
scale_fill_viridis_c(
option = "viridis",
direction = -1,
limits = c(min, max),
guide = "none"
) +
theme(legend.position = c(1, 1)) + theme(
legend.position = "right",
legend.box = "vertical",
text = element_text(size = 50),
legend.key.size = unit(0.9, 'cm')
)
ggsave(
file = "output/heatmap_Uralic_informativity.svg",
plot = p1,
width = 7,
height = 7,
dpi=300
)
triple_plot <-
b_labelled / i_labelled | p1 #+ plot_annotation(tag_levels = '1')
ggsave(
file = "output/triple_plot.svg",
plot = triple_plot,
width = 12,
height = 7,
dpi=300
)
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