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.Rhistory
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/ its2ProfsPerc$sum))
head(its2ProfsPerc)
apply(its2ProfsPerc[, c(10:(ncol(its2ProfsPerc)))], 1, function(x) {
sum(x, na.rm = T)
})
head(its2ProfsPerc)
gssProf = otuStack(its2ProfsPerc, count.columns = c(10:length(its2ProfsPerc[1, ])),
condition.columns = c(1:9)) # remove summ rows
gssProf = gssProf %>% filter(otu != "summ") %>% droplevels()
levels(gssProf$otu)
levels(gssProf$depthZoneM)
levels(gssProf$depthZoneM) = c("10 m", "15 m", "25 m", "35 m")
levels(gssProf$site)
levels(gssProf$site) = c("Alacranes", "Bajos del Norte")
levels(gssProf$depthZoneM)
levels(gssProf$site)
its2ProfsPlotA = ggplot(gssProf, aes(x = barPlotOrder, y = count, fill = factor(otu))) +
geom_bar(position = "stack", stat = "identity", color = "black", size = 0.25) +
ylab("Proportion") +
scale_fill_paletteer_d("dichromat::Categorical_12")+
labs(fill = expression(paste(italic("ITS2"), " type profile"))) +
guides(fill = guide_legend(ncol = 2, reverse = FALSE)) +
facet_grid(depthZoneM ~ site, scales = "free_x") + #faceting plots by Depth and Site
theme_bw()
its2ProfsPlot = its2ProfsPlotA +
theme(axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y=element_blank(),
legend.position = "bottom",
legend.title = element_text(color = "black", size = 12, hjust = 0.5, angle = 90),
legend.text = element_text(color = "black", size = 10),
legend.key = element_blank(),
legend.key.size = unit(0.75,"line"),
legend.background = element_blank(),
# panel.border = element_blank(),
# panel.background = element_rect(fill = "white"),
panel.grid=element_blank(),
panel.background=element_rect(fill=NA, colour="grey25"),
panel.spacing.x=grid:::unit(0, "lines"),
panel.border = element_rect(fill=NA,color="black", size=2, linetype="solid"),
plot.background = element_blank(),
strip.text.x = element_text(size = 12),
strip.text.y = element_text(size = 12),
strip.background = element_rect(fill = "white", size = 0.9)
)
its2ProfsPlot
ggsave("./figures/fig5.png", plot = its2ProfsPlot, width = 8.5, height = 8.5, unit = "in", dpi = 600)
its2ProfsPlot = its2ProfsPlotA +
theme(axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y=element_blank(),
legend.position = "bottom",
legend.title = element_text(color = "black", size = 12, hjust = 0.5, angle = 90),
legend.text = element_text(color = "black", size = 10),
legend.key = element_blank(),
legend.key.size = unit(0.75,"line"),
legend.background = element_blank(),
# panel.border = element_blank(),
# panel.background = element_rect(fill = "white"),
panel.grid=element_blank(),
panel.background=element_rect(fill=NA, colour="grey25"),
panel.spacing.x=grid:::unit(0, "lines"),
panel.border = element_rect(fill=NA,color="black", size=1, linetype="solid"),
plot.background = element_blank(),
strip.text.x = element_text(size = 12),
strip.text.y = element_text(size = 12),
strip.background = element_rect(fill = "white", size = 0.9)
)
its2ProfsPlot
ggsave("./figures/fig5.png", plot = its2ProfsPlot, width = 8.5, height = 8.5, unit = "in", dpi = 600)
its2ProfsPlot = its2ProfsPlotA +
theme(axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y=element_blank(),
legend.position = "bottom",
legend.title = element_text(color = "black", size = 12, hjust = 0.5, angle = 90),
legend.text = element_text(color = "black", size = 10),
legend.key = element_blank(),
legend.key.size = unit(0.75,"line"),
legend.background = element_blank(),
# panel.border = element_blank(),
# panel.background = element_rect(fill = "white"),
panel.grid=element_blank(),
panel.background=element_rect(fill=NA, colour="grey25"),
panel.spacing.x=grid:::unit(0, "lines"),
panel.border = element_rect(fill=NA,color="black", size=1, linetype="solid"),
plot.background = element_blank(),
strip.text.x = element_text(size = 12),
strip.text.y = element_text(size = 12),
strip.background = element_rect(fill = "white", size = 1)
)
ggsave("./figures/fig5.png", plot = its2ProfsPlot, width = 8.5, height = 8.5, unit = "in", dpi = 600)
its2ProfsPlotA = ggplot(gssProf, aes(x = barPlotOrder, y = count, fill = factor(otu))) +
geom_bar(position = "stack", stat = "identity", color = "black", size = 0.25) +
ylab("Proportion") +
scale_fill_paletteer_d("dichromat::Categorical_12")+
labs(fill = expression(paste(italic("ITS2"), " type profile"))) +
guides(fill = guide_legend(ncol = 2, reverse = FALSE)) +
facet_grid(depthZoneM ~ site, scales = "free_x") +#faceting plots by Depth and Site
coord_cartesian()+
theme_bw()
its2ProfsPlot = its2ProfsPlotA +
theme(axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y=element_blank(),
legend.position = "bottom",
legend.title = element_text(color = "black", size = 12, hjust = 0.5, angle = 90),
legend.text = element_text(color = "black", size = 10),
legend.key = element_blank(),
legend.key.size = unit(0.75,"line"),
legend.background = element_blank(),
# panel.border = element_blank(),
# panel.background = element_rect(fill = "white"),
panel.grid=element_blank(),
panel.background=element_rect(fill=NA, colour="grey25"),
panel.spacing.x=grid:::unit(0, "lines"),
panel.border = element_rect(fill=NA,color="black", size=1, linetype="solid"),
plot.background = element_blank(),
strip.text.x = element_text(size = 12),
strip.text.y = element_text(size = 12),
strip.background = element_rect(fill = "white", size = 1)
)
its2ProfsPlot
its2ProfsPlotA = ggplot(gssProf, aes(x = barPlotOrder, y = count, fill = factor(otu))) +
geom_bar(position = "stack", stat = "identity", color = "black", size = 0.25) +
ylab("Proportion") +
scale_fill_paletteer_d("dichromat::Categorical_12")+
labs(fill = expression(paste(italic("ITS2"), " type profile"))) +
guides(fill = guide_legend(ncol = 2, reverse = FALSE)) +
facet_grid(depthZoneM ~ site, scales = "free_x") +#faceting plots by Depth and Site
coord_cartesian(clip = TRUE)+
theme_bw()
its2ProfsPlot = its2ProfsPlotA +
theme(axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y=element_blank(),
legend.position = "bottom",
legend.title = element_text(color = "black", size = 12, hjust = 0.5, angle = 90),
legend.text = element_text(color = "black", size = 10),
legend.key = element_blank(),
legend.key.size = unit(0.75,"line"),
legend.background = element_blank(),
# panel.border = element_blank(),
# panel.background = element_rect(fill = "white"),
panel.grid=element_blank(),
panel.background=element_rect(fill=NA, colour="grey25"),
panel.spacing.x=grid:::unit(0, "lines"),
panel.border = element_rect(fill=NA,color="black", size=1, linetype="solid"),
plot.background = element_blank(),
strip.text.x = element_text(size = 12),
strip.text.y = element_text(size = 12),
strip.background = element_rect(fill = "white", size = 1)
)
its2ProfsPlot
its2ProfsPlotA = ggplot(gssProf, aes(x = barPlotOrder, y = count, fill = factor(otu))) +
geom_bar(position = "stack", stat = "identity", color = "black", size = 0.25) +
ylab("Proportion") +
scale_fill_paletteer_d("dichromat::Categorical_12")+
labs(fill = expression(paste(italic("ITS2"), " type profile"))) +
guides(fill = guide_legend(ncol = 2, reverse = FALSE)) +
facet_grid(depthZoneM ~ site, scales = "free_x") +#faceting plots by Depth and Site
scale_x_discrete(expand=c(0, 0)) +
scale_y_continuous(expand=c(0, 0)) +
theme_bw()
its2ProfsPlot = its2ProfsPlotA +
theme(axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y=element_blank(),
legend.position = "bottom",
legend.title = element_text(color = "black", size = 12, hjust = 0.5, angle = 90),
legend.text = element_text(color = "black", size = 10),
legend.key = element_blank(),
legend.key.size = unit(0.75,"line"),
legend.background = element_blank(),
# panel.border = element_blank(),
# panel.background = element_rect(fill = "white"),
panel.grid=element_blank(),
panel.background=element_rect(fill=NA, colour="grey25"),
panel.spacing.x=grid:::unit(0, "lines"),
panel.border = element_rect(fill=NA,color="black", size=1, linetype="solid"),
plot.background = element_blank(),
strip.text.x = element_text(size = 12),
strip.text.y = element_text(size = 12),
strip.background = element_rect(fill = "white", size = 1)
)
ggsave("./figures/fig5.png", plot = its2ProfsPlot, width = 8.5, height = 8.5, unit = "in", dpi = 600)
p2 = ggplot(data = subset(mdat, subset = mdat$Ancestry %in% c("cluster2.1", "cluster2.2")), aes(x=barPlotOrder, y=Fraction, fill=Ancestry, order=barPlotOrder)) +
geom_bar(stat="identity", position="fill", width=1, colour="grey25") +
#facet_grid(.~site, scales = "free", switch = "x", space = "free") +
facet_grid(depthZoneM ~ site, scales = "free") + #faceting plots by Depth and Site
labs(x = "Population", y = "Ancestry") +
ggtitle(expression(paste(italic("K"), "=2"))) +
theme(plot.title = element_text(size=40),
panel.grid=element_blank(),
panel.background=element_rect(fill=NA, colour="grey25"),
panel.spacing.x=grid:::unit(0, "lines"),
panel.border = element_rect(fill=NA,color="black", size=1, linetype="solid"),
axis.text.x=element_blank(),
axis.text.y = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank(),
axis.ticks.x=element_blank(),
axis.ticks.y=element_blank(),
strip.background = element_rect(fill = "white", size = 1, color="black"),
strip.text.x = element_text(size = 30),
strip.text.y = element_blank(),
#strip.text=element_text(size=20, angle=90),
legend.key=element_blank(),
legend.position = "none",
legend.title = element_blank()) +
scale_x_discrete(expand=c(0, 0)) +
scale_y_continuous(expand=c(0, 0)) +
#scale_fill_manual(values = brewer.pal(name = "YlGnBu", n = 4), name = "Cluster") +
scale_fill_manual(values = colPal2, name = "Cluster") +
guides(fill=guide_legend(override.aes=list(colour=NULL)))
p2 = ggplot(data = subset(mdat, subset = mdat$Ancestry %in% c("cluster2.1", "cluster2.2")), aes(x=barPlotOrder, y=Fraction, fill=Ancestry, order=barPlotOrder)) +
geom_bar(stat="identity", position="fill", width=1, colour="grey25") +
#facet_grid(.~site, scales = "free", switch = "x", space = "free") +
facet_grid(depthZoneM ~ site, scales = "free") + #faceting plots by Depth and Site
labs(x = "Population", y = "Ancestry") +
ggtitle(expression(paste(italic("K"), "=2"))) +
theme(plot.title = element_text(size=40),
panel.grid=element_blank(),
panel.background=element_rect(fill=NA, colour="grey25"),
panel.spacing.x=grid:::unit(0, "lines"),
panel.border = element_rect(fill=NA,color="black", size=1, linetype="solid"),
axis.text.x=element_blank(),
axis.text.y = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank(),
axis.ticks.x=element_blank(),
axis.ticks.y=element_blank(),
strip.background = element_rect(fill = "white", size = 1, color="black"),
strip.text.x = element_text(size = 30),
strip.text.y = element_blank(),
#strip.text=element_text(size=20, angle=90),
legend.key=element_blank(),
legend.position = "none",
legend.title = element_blank()) +
scale_x_discrete(expand=c(0, 0)) +
scale_y_continuous(expand=c(0, 0)) +
#scale_fill_manual(values = brewer.pal(name = "YlGnBu", n = 4), name = "Cluster") +
scale_fill_manual(values = colPal2, name = "Cluster") +
guides(fill=guide_legend(override.aes=list(colour=NULL)))
paletteer_d("NineteenEightyR::miami2")
colPal2=c("turquoise", "yellow")
#colPal2=c("#3FB8AFFF", "#DAD8A7FF")
mxNgsAdmix <- read.csv("mxMcavNoClones_k2k3.csv") %>% arrange(site, depthZoneM, -cluster2.2)
# mxK2$sample = factor(mxK2$sample, levels = mxK2$sample[order(-mxK2$cluster2)])
sampleCounts = plyr::count(mxNgsAdmix, c('site','depthZoneM'))
meltedList = reshape2::melt(lapply(sampleCounts$freq,function(x){c(1:x)}))
mxNgsAdmix$barPlotOrder = meltedList$value
mxNgsAdmix$depthZoneM=as.factor(mxNgsAdmix$depthZoneM)
mdat = melt(mxNgsAdmix, id.vars=c("sample", "site", "depthZoneM", "barPlotOrder"), variable.name="Ancestry", value.name="Fraction")
#mdat2$site=as.factor(mdat2$site)
mdat$depthZoneM=as.factor(mdat$depthZoneM)
levels(mdat$depthZoneM)
levels(mdat$depthZoneM) = c("10 m", "15 m", "25 m", "35 m")
p2 = ggplot(data = subset(mdat, subset = mdat$Ancestry %in% c("cluster2.1", "cluster2.2")), aes(x=barPlotOrder, y=Fraction, fill=Ancestry, order=barPlotOrder)) +
geom_bar(stat="identity", position="fill", width=1, colour="grey25") +
#facet_grid(.~site, scales = "free", switch = "x", space = "free") +
facet_grid(depthZoneM ~ site, scales = "free") + #faceting plots by Depth and Site
labs(x = "Population", y = "Ancestry") +
ggtitle(expression(paste(italic("K"), "=2"))) +
theme(plot.title = element_text(size=40),
panel.grid=element_blank(),
panel.background=element_rect(fill=NA, colour="grey25"),
panel.spacing.x=grid:::unit(0, "lines"),
panel.border = element_rect(fill=NA,color="black", size=1, linetype="solid"),
axis.text.x=element_blank(),
axis.text.y = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank(),
axis.ticks.x=element_blank(),
axis.ticks.y=element_blank(),
strip.background = element_rect(fill = "white", size = 1, color="black"),
strip.text.x = element_text(size = 30),
strip.text.y = element_blank(),
#strip.text=element_text(size=20, angle=90),
legend.key=element_blank(),
legend.position = "none",
legend.title = element_blank()) +
scale_x_discrete(expand=c(0, 0)) +
scale_y_continuous(expand=c(0, 0)) +
#scale_fill_manual(values = brewer.pal(name = "YlGnBu", n = 4), name = "Cluster") +
scale_fill_manual(values = colPal2, name = "Cluster") +
guides(fill=guide_legend(override.aes=list(colour=NULL)))
p2
###########
colPal3=c("turquoise", "yellow", "hot pink")
#colPal3=c("#3FB8AFFF", "#DAD8A7FF", "#FF3D7FFF")
# mxK3 <- read.csv("mxMcavNoClones_K3.csv") %>% arrange(pop, depthZoneM, -cluster2)
# # mxK3$sample = factor(mxK3$sample, levels = mxK3$sample[order(-mxK3$cluster2)])
# sampleCountsK3 = plyr::count(mxK3, c('pop','depthZoneM'))
# meltedListK3 = reshape2::melt(lapply(sampleCountsK3$freq,function(x){c(1:x)}))
#
# mxK3$barPlotOrderK3 = meltedListK3$value
# mdat3 = melt(mxK3, id.vars=c("sample", "pop", "depthZoneM", "barPlotOrderK3"), variable.name="Ancestry", value.name="Fraction")
# #mdat2$pop=as.factor(mdat3$pop)
# mdat3$depthZoneM=as.factor(mdat3$depthZoneM)
# levels(mdat3$depthZoneM)
# levels(mdat3$depthZoneM) = c("10 m", "15 m", "25 m", "35 m")
p3 = ggplot(data = subset(mdat, subset = mdat$Ancestry %in% c("cluster3.1", "cluster3.2", "cluster3.3")), aes(x=barPlotOrder, y=Fraction, fill=Ancestry, order=barPlotOrder)) +
geom_bar(stat="identity", position="fill", width=1, colour="grey25") +
#facet_grid(.~pop, scales = "free", switch = "x", space = "free") +
facet_grid(depthZoneM ~ site, scales = "free") + #faceting plots by Depth and Site
labs(x = "Population", y = "Ancestry") +
ggtitle(expression(paste(italic("K"), "=3"))) +
theme(plot.title = element_text(size=40),
panel.grid=element_blank(),
panel.background=element_rect(fill=NA, colour="grey25"),
panel.spacing.x=grid:::unit(0, "lines"),
panel.border = element_rect(fill=NA,color="black", size=2, linetype="solid"),
axis.text.x=element_blank(),
axis.text.y = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank(),
axis.ticks.x=element_blank(),
axis.ticks.y=element_blank(),
strip.background = element_rect(fill = "white", size = 0.9, color="black"),
strip.text.x = element_text(size = 30),
strip.text.y = element_text(size = 30),
#strip.text=element_text(size=20, angle=90),
legend.key=element_blank(),
legend.position = "none",
legend.title = element_blank()) +
scale_x_discrete(expand=c(0, 0)) +
scale_y_continuous(expand=c(0, 0)) +
#scale_fill_manual(values = brewer.pal(name = "YlGnBu", n = 4), name = "Cluster") +
scale_fill_manual(values = colPal3, name = "Cluster") +
guides(fill=guide_legend(override.aes=list(colour=NULL)))
p3
combinedAdmix = (p2 | p3)
combinedAdmix
ggsave("./figures/fig4.png", plot = combinedAdmix, width = 70, height = 40, units = "cm", dpi = 300)
p3 = ggplot(data = subset(mdat, subset = mdat$Ancestry %in% c("cluster3.1", "cluster3.2", "cluster3.3")), aes(x=barPlotOrder, y=Fraction, fill=Ancestry, order=barPlotOrder)) +
geom_bar(stat="identity", position="fill", width=1, colour="grey25") +
#facet_grid(.~pop, scales = "free", switch = "x", space = "free") +
facet_grid(depthZoneM ~ site, scales = "free") + #faceting plots by Depth and Site
labs(x = "Population", y = "Ancestry") +
ggtitle(expression(paste(italic("K"), "=3"))) +
theme(plot.title = element_text(size=40),
panel.grid=element_blank(),
panel.background=element_rect(fill=NA, colour="grey25"),
panel.spacing.x=grid:::unit(0, "lines"),
panel.border = element_rect(fill=NA,color="black", size=1, linetype="solid"),
axis.text.x=element_blank(),
axis.text.y = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank(),
axis.ticks.x=element_blank(),
axis.ticks.y=element_blank(),
strip.background = element_rect(fill = "white", size = 1, color="black"),
strip.text.x = element_text(size = 30),
strip.text.y = element_text(size = 30),
#strip.text=element_text(size=20, angle=90),
legend.key=element_blank(),
legend.position = "none",
legend.title = element_blank()) +
scale_x_discrete(expand=c(0, 0)) +
scale_y_continuous(expand=c(0, 0)) +
#scale_fill_manual(values = brewer.pal(name = "YlGnBu", n = 4), name = "Cluster") +
scale_fill_manual(values = colPal3, name = "Cluster") +
guides(fill=guide_legend(override.aes=list(colour=NULL)))
combinedAdmix = (p2 | p3)
combinedAdmix
ggsave("./figures/fig4.png", plot = combinedAdmix, width = 70, height = 40, units = "cm", dpi = 300)
paletteer_d("NineteenEightyR::miami2")
colPal2=c("turquoise", "yellow")
#colPal2=c("#3FB8AFFF", "#DAD8A7FF")
mxNgsAdmix <- read.csv("mxMcavNoClones_k2k3.csv") %>% arrange(site, depthZoneM, -cluster2.2)
# mxK2$sample = factor(mxK2$sample, levels = mxK2$sample[order(-mxK2$cluster2)])
sampleCounts = plyr::count(mxNgsAdmix, c('site','depthZoneM'))
meltedList = reshape2::melt(lapply(sampleCounts$freq,function(x){c(1:x)}))
mxNgsAdmix$barPlotOrder = meltedList$value
mxNgsAdmix$depthZoneM=as.factor(mxNgsAdmix$depthZoneM)
mdat = melt(mxNgsAdmix, id.vars=c("sample", "site", "depthZoneM", "barPlotOrder"), variable.name="Ancestry", value.name="Fraction")
#mdat2$site=as.factor(mdat2$site)
mdat$depthZoneM=as.factor(mdat$depthZoneM)
levels(mdat$depthZoneM)
levels(mdat$depthZoneM) = c("10 m", "15 m", "25 m", "35 m")
p2 = ggplot(data = subset(mdat, subset = mdat$Ancestry %in% c("cluster2.1", "cluster2.2")), aes(x=barPlotOrder, y=Fraction, fill=Ancestry, order=barPlotOrder)) +
geom_bar(stat="identity", position="fill", width=1, colour="grey25") +
#facet_grid(.~site, scales = "free", switch = "x", space = "free") +
facet_grid(depthZoneM ~ site, scales = "free") + #faceting plots by Depth and Site
labs(x = "Population", y = "Ancestry") +
ggtitle(expression(paste(italic("K"), "=2"))) +
theme(plot.title = element_text(size=40),
panel.grid=element_blank(),
panel.background=element_rect(fill=NA, colour="grey25"),
panel.spacing.x=grid:::unit(0, "lines"),
panel.border = element_rect(fill=NA,color="black", size=2, linetype="solid"),
axis.text.x=element_blank(),
axis.text.y = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank(),
axis.ticks.x=element_blank(),
axis.ticks.y=element_blank(),
strip.background = element_rect(fill = "white", size = 2, color="black"),
strip.text.x = element_text(size = 30),
strip.text.y = element_blank(),
#strip.text=element_text(size=20, angle=90),
legend.key=element_blank(),
legend.position = "none",
legend.title = element_blank()) +
scale_x_discrete(expand=c(0, 0)) +
scale_y_continuous(expand=c(0, 0)) +
#scale_fill_manual(values = brewer.pal(name = "YlGnBu", n = 4), name = "Cluster") +
scale_fill_manual(values = colPal2, name = "Cluster") +
guides(fill=guide_legend(override.aes=list(colour=NULL)))
p2
###########
colPal3=c("turquoise", "yellow", "hot pink")
#colPal3=c("#3FB8AFFF", "#DAD8A7FF", "#FF3D7FFF")
# mxK3 <- read.csv("mxMcavNoClones_K3.csv") %>% arrange(pop, depthZoneM, -cluster2)
# # mxK3$sample = factor(mxK3$sample, levels = mxK3$sample[order(-mxK3$cluster2)])
# sampleCountsK3 = plyr::count(mxK3, c('pop','depthZoneM'))
# meltedListK3 = reshape2::melt(lapply(sampleCountsK3$freq,function(x){c(1:x)}))
#
# mxK3$barPlotOrderK3 = meltedListK3$value
# mdat3 = melt(mxK3, id.vars=c("sample", "pop", "depthZoneM", "barPlotOrderK3"), variable.name="Ancestry", value.name="Fraction")
# #mdat2$pop=as.factor(mdat3$pop)
# mdat3$depthZoneM=as.factor(mdat3$depthZoneM)
# levels(mdat3$depthZoneM)
# levels(mdat3$depthZoneM) = c("10 m", "15 m", "25 m", "35 m")
p3 = ggplot(data = subset(mdat, subset = mdat$Ancestry %in% c("cluster3.1", "cluster3.2", "cluster3.3")), aes(x=barPlotOrder, y=Fraction, fill=Ancestry, order=barPlotOrder)) +
geom_bar(stat="identity", position="fill", width=1, colour="grey25") +
#facet_grid(.~pop, scales = "free", switch = "x", space = "free") +
facet_grid(depthZoneM ~ site, scales = "free") + #faceting plots by Depth and Site
labs(x = "Population", y = "Ancestry") +
ggtitle(expression(paste(italic("K"), "=3"))) +
theme(plot.title = element_text(size=40),
panel.grid=element_blank(),
panel.background=element_rect(fill=NA, colour="grey25"),
panel.spacing.x=grid:::unit(0, "lines"),
panel.border = element_rect(fill=NA,color="black", size=2, linetype="solid"),
axis.text.x=element_blank(),
axis.text.y = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank(),
axis.ticks.x=element_blank(),
axis.ticks.y=element_blank(),
strip.background = element_rect(fill = "white", size = 2, color="black"),
strip.text.x = element_text(size = 30),
strip.text.y = element_text(size = 30),
#strip.text=element_text(size=20, angle=90),
legend.key=element_blank(),
legend.position = "none",
legend.title = element_blank()) +
scale_x_discrete(expand=c(0, 0)) +
scale_y_continuous(expand=c(0, 0)) +
#scale_fill_manual(values = brewer.pal(name = "YlGnBu", n = 4), name = "Cluster") +
scale_fill_manual(values = colPal3, name = "Cluster") +
guides(fill=guide_legend(override.aes=list(colour=NULL)))
p3
combinedAdmix = (p2 | p3)
combinedAdmix
ggsave("./figures/fig4.png", plot = combinedAdmix, width = 70, height = 40, units = "cm", dpi = 300)
its2ProfsPlotA = ggplot(gssProf, aes(x = barPlotOrder, y = count, fill = factor(otu))) +
geom_bar(position = "stack", stat = "identity", color = "black", size = 0.25, width = 1) +
ylab("Proportion") +
scale_fill_paletteer_d("dichromat::Categorical_12")+
labs(fill = expression(paste(italic("ITS2"), " type profile"))) +
guides(fill = guide_legend(ncol = 2, reverse = FALSE)) +
facet_grid(depthZoneM ~ site, scales = "free_x") +#faceting plots by Depth and Site
scale_x_discrete(expand=c(0, 0)) +
scale_y_continuous(expand=c(0, 0)) +
theme_bw()
its2ProfsPlot = its2ProfsPlotA +
theme(axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y=element_blank(),
legend.position = "bottom",
legend.title = element_text(color = "black", size = 12, hjust = 0.5, angle = 90),
legend.text = element_text(color = "black", size = 10),
legend.key = element_blank(),
legend.key.size = unit(0.75,"line"),
legend.background = element_blank(),
# panel.border = element_blank(),
# panel.background = element_rect(fill = "white"),
panel.grid=element_blank(),
panel.background=element_rect(fill=NA, colour="grey25"),
panel.spacing.x=grid:::unit(0, "lines"),
panel.border = element_rect(fill=NA,color="black", size=1, linetype="solid"),
plot.background = element_blank(),
strip.text.x = element_text(size = 12),
strip.text.y = element_text(size = 12),
strip.background = element_rect(fill = "white", size = 1)
)
its2ProfsPlot
ggsave("./figures/fig5.png", plot = its2ProfsPlot, width = 8.5, height = 8.5, unit = "in", dpi = 600)