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XX_combined_plots_beta.R
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Multi-panel figure - BETA DIVERSITY (nMDS and pw Bray-Curtis boxplot)
#
# Combine results from different scripts into single
# plots to have consistent layouts (for publication).
#
# Used rarefied x 1000 data!
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
library(tidyverse)
library(here)
# Palette
source("colors_GfasMS.R")
# BETA diversity (nMDS's + boxplot of B-C pwd) ------------------------
## Import .rds ----------------
# nMDS
all <- readRDS("./out/RDS_files/nMDS_bray1000.rds")
ordn_bray_all <- readRDS("./out/RDS_files/ordn1000_bray_all.rds")
RS <- readRDS("./out/RDS_files/nMDS_bray1000_RS.rds")
ordn_bray_RS <- readRDS("./out/RDS_files/ordn1000_bray_RS.rds")
HK <- readRDS("./out/RDS_files/nMDS_bray1000_HK.rds")
ordn_bray_HK <- readRDS("./out/RDS_files/ordn1000_bray_HK.rds")
# pw Bray-Curtis boxplot
pwcBC_n3 <- readRDS("./out/RDS_files/pwcBC1000_n3_tibble.rds")
w_n3 <- readRDS("./out/RDS_files/rar1000_w_n3.rds")
## Ordination plots: general settings for plots --------------
theme_set(theme_bw())
### Figure 2 A - NEW (colony by shape) ----------------------------------------------
# Text: test results
# Plot
(nMDS_all_shapes <- ggplot() +
stat_ellipse(data = all,
aes(x = MDS1, y = MDS2,
color = origin_ms),
level = 0.95,
size = 0.5,
show.legend = F) +
scale_color_manual(breaks = c("Red Sea", "Hong Kong"),
values = c(Red_Sea, Hong_Kong),
guide = "none") +
ggnewscale::new_scale_color() +
geom_point(data = all,
inherit.aes = F,
aes(x = MDS1, y = MDS2,
color = colony_ms,
shape = colony_ms,
fill = state
),
stroke = 1) +
scale_shape_manual(
breaks = c("RS1", "RS2", "RS3", "HK1", "HK2"),
values = c(21:25)
) +
scale_fill_manual(
breaks = c("symbiotic", "bleached"),
values = c("black", "white"), # then manually replace in Inkscape ...
labels = c("Symbiotic", "Bleached")) +
scale_color_manual(values = palette_GfasMS,
guide = guide_legend(order = 2)) +
labs(
subtitle = paste0("Stress = ", round(ordn_bray_all$stress, 3))
) +
scale_x_continuous(breaks = seq(-0.5, 0.5, by = 0.5)) +
scale_y_continuous(breaks = seq(-0.5, 0.5, by = 0.5)) +
coord_fixed(ratio = 1, # necessary for correct ratio of axes!
xlim = NULL, ylim = NULL, expand = TRUE, clip = "on") +
theme(
panel.grid = element_blank(),
plot.subtitle = element_text(hjust = 0.02, vjust = -10,
size = 6,
color = "black"), # top left
text = element_text(size = 13),
axis.text = element_text(size = 10, colour = "black"),
axis.title = element_text(size = 10),
legend.title = element_blank() ,
legend.position = "none"
)
)
ggsave("./out/Gfas_16S/beta_diversity/rar1000_nMDS_originellipses_all_shapes.png",
# bg = "white",
dpi = 330,
units = "cm", width = 15.5, height = 12.5)
### Figure 2 B - NEW (pw B-C dist, boxplot) ----------------------------------------------
# Text: test results
wlcx_md <- paste0("Mann-Whitney U test<br>",
"*W* = ", w_n3$statistic, ", *P* = **", # w_n3$method
format(round(w_n3$p.value, 4), scientific = F),
"**")
# Plot
(
pwcBDn3_shapes <- ggplot(pwcBC_n3, aes(
x = forcats::fct_rev(state),
y = pairwise_distance,
color = colony_ms,
shape = colony_ms,
fill = state)) +
geom_boxplot(inherit.aes = F,
aes(x = forcats::fct_rev(state),
y = pairwise_distance),
show.legend = F,
color = "grey69",
outlier.shape = NA,
) +
ggbeeswarm::geom_quasirandom(aes(fill = state),
width = 0.2,
stroke = 1) + # 1.5
scale_color_manual(values = palette_GfasMS) +
scale_fill_manual(breaks = c("S", "B"),
values = c("black", "white"),
labels = c("Symbiotic", "Bleached")) +
scale_shape_manual(
breaks = c("RS1", "RS2", "RS3", "HK1", "HK2"),
values = c(21:25)) +
scale_x_discrete(breaks = c("S", "B"),
labels = c("Symbiotic", "Bleached")) +
labs(
y = "Bray-Curtis pairwise distance",
color = "Colony",
shape = "Colony",
fill = "State"
) +
ggtext::geom_richtext(aes(x = 0.5, y = 0.9,
label = wlcx_md),
stat = "unique",
color = "black", fill = NA,
label.color = NA,
size = 2,
hjust = 0 ) +
theme(
axis.title.x = element_blank(),
axis.text.x = element_text(color = "black", size = 10),
axis.title = element_text(size = 10),
panel.grid = element_blank(),
legend.title = element_text(size = 7),
legend.text = element_text(size = 6),
legend.position = "right",
legend.justification = "top",
aspect.ratio = 2
) +
guides(
fill = guide_legend(
override.aes = list(
shape = c(21, 21)) ))
)
ggsave("./out/Gfas_16S/beta_diversity/rar1000_pwcBDn3_shapes.png",
# bg = "white",
dpi = 330,
units = "cm", width = 15.5, height = 12.5)
## Panel figures -----------------
### TOP: nMDS_all + pwc_BC_n3 ------------------------
#### .{Patchwork} - good -------------------------------
library(patchwork)
(
AB <- nMDS_all_shapes + pwcBDn3_shapes
)
ggsave("./out/Gfas_16S/beta_diversity/rar1000_nMDSall_pwBCn3_legendR_shapes.png",
# bg = "white",
dpi = 330,
units = "cm", width = 18, height = 10) # Keep dimensions to match with CD panels (patchwork below)
ggsave("./out/Gfas_16S/beta_diversity/rar1000_nMDSall_pwBCn3_legendR_shapes.svg",
# bg = "white",
dpi = 330,
units = "cm", width = 18, height = 10) # Keep dimensions to match with CD panels (patchwork below)
##### Shape by colony & Legend outside ----------------------
# facet combine nMDS data
RSHK <- bind_rows(RS, HK)
(nMDS_RSHK_out <- ggplot(data = RSHK,
aes(x = MDS1,
y = MDS2,
# shape = state,
fill = state,
shape = colony_ms,
group = state,
linetype = state,
color = origin_ms)) +
geom_point() +
scale_shape_manual(
breaks = c("RS1", "RS2", "RS3", "HK1", "HK2"),
values = c(21:25)
# labels = c("Symbiotic", "Bleached")
) +
scale_fill_manual(
breaks = c("symbiotic", "bleached"),
values = c(Red_Sea, "white"),
labels = c("Symbiotic", "Bleached")) +
stat_ellipse(level = 0.95,
size = 0.5) +
scale_linetype_manual(
breaks = c("symbiotic", "bleached"),
values = c("solid", "dotted"),
labels = c("Symbiotic", "Bleached")
) +
scale_color_manual(values = c(Red_Sea, Hong_Kong),
breaks = c( "Red Sea", "Hong Kong")) +
coord_fixed(ratio = 1, # necessary for correct ratio of axes!
xlim = NULL, ylim = NULL, expand = TRUE, clip = "on") +
theme_bw() +
theme(
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
legend.title = element_blank(),
legend.position = "bottom",
legend.box = "vertical",
legend.background = element_rect(fill = NA),
legend.spacing = unit(0.1, 'cm'),
legend.key.size = unit(0.5, 'cm'),
strip.background = element_rect(fill = NA, colour = NA),
strip.text = element_text(face = "bold")
) +
facet_wrap(~fct_rev(origin_ms)) +
guides(
fill = guide_legend(
override.aes = list(
shape = 21,
linetype = c("solid", "dotted")) )
)
)
ggsave("./out/Gfas_16S/beta_diversity/rar1000_Bray_nMDS_ellipses_colonyshape_RSHK.png",
bg = "white",
dpi = 330,
units = "cm", width = 17, height = 15)
ggsave("./out/Gfas_16S/beta_diversity/rar1000_Bray_nMDS_ellipses_colonyshape_RSHK.svg",
bg = "white",
dpi = 330,
units = "cm", width = 17, height = 15)
### For SUPPLEMENTARY ------------------------------
#### nMDS with ellipses by STATE -----------------
# show overlapping ellipses = won't find a significant difference with PERMDISP
# nor PERMANOVA (see "PERMANOVA with vegan::ADONIS2" lines 386-435)
ggplot(data = all, # nMDS_bray
aes(x = MDS1,
y = MDS2,
shape = state,
group = state, linetype = state)) +
geom_point() +
scale_shape_manual(
breaks = c("symbiotic", "bleached"),
values = c(16, 1),
labels = c("Symbiotic", "Bleached")) +
stat_ellipse(level = 0.95,
size = 0.5) +
scale_linetype_manual(
breaks = c("symbiotic", "bleached"),
values = c("solid", "dotted"),
labels = c("Symbiotic", "Bleached")) +
scale_x_continuous(
breaks = seq(-0.5, 0.5, by = 0.5)) +
scale_y_continuous(
breaks = seq(-0.5, 0.5, by = 0.5)) +
coord_fixed(ratio = 1, # necessary for correct ratio of axes!
xlim = NULL, ylim = NULL, expand = TRUE, clip = "on") +
theme_classic() +
theme(
legend.title = element_blank(),
legend.justification = "top"
)
ggsave("./out/Gfas_16S/beta_diversity/rar1000_Bray_nMDS_ellipses_state.png",
bg = "white",
dpi = 330,
units = "cm", width = 15.5, height = 12.5)