Revision 6b13e7adea800e7cb2dbae5ca3f6ace83db298ea authored by morgankain on 30 April 2021, 20:35:51 UTC, committed by morgankain on 30 April 2021, 20:35:51 UTC
1 parent 7d3f6ce
24_manuscript_plots_fig2_panels.R
###################################################################
### various individual plots for the various panels of figure 2 ###
###################################################################
####
## Host panel 1, just AUC of the hosts in the community
####
ggplot(AUC_titer.gg.s, aes(est, Host)) +
geom_point(lwd = 0.50) +
geom_errorbarh(aes(xmin = lwr, xmax = upr, y = Host), height = 0.5, lwd = 0.3) +
ylab("Host Species") +
xlab("AUC Titer Profile") +
theme(
panel.grid = element_blank()
, panel.border = element_rect(colour = "black", fill = NA, size = 0)
, axis.line = element_line()
, axis.text.y = element_text(size = 10)
, axis.text.x = element_text(size = 10)
, axis.title.x = element_text(size = 12)
, axis.title.y = element_text(size = 12)
)
ggsave(filename = "/Users/Morgan/Desktop/host_A.pdf", plot = last_plot(), width = 2.2, height = 2.24, units = c("in"))
####
## Mosquito panel 1, just AUC of the mosquitoes in the community
####
ggplot(mosq_inf_AUC_all_samps_adj_to_com.gg.s, aes(est, mosq)) +
geom_point(lwd = 0.50) +
geom_errorbarh(aes(xmin = lwr, xmax = upr, y = mosq), height = 0.5, lwd = 0.3) +
scale_x_continuous(breaks = c(0, 30, 60, 120)) +
ylab("Mosquito Species") +
xlab("AUC Infection
Probability *
AUC Transmission
Probability") +
theme(
panel.grid = element_blank()
, panel.border = element_rect(colour = "black", fill = NA, size = 0)
, axis.line = element_line()
, axis.text.y = element_text(size = 8)
, axis.text.x = element_text(size = 10)
, axis.title.x = element_text(size = 10)
, axis.title.y = element_text(size = 12)
)
ggsave(filename = "/Users/Morgan/Desktop/mosq_A.pdf", plot = last_plot(), width = 2.3, height = 2.65, units = c("in"))
####
## Host panel 2, Host to Mosquito transmission matrix and summary CI plot
####
## The summary part of the panel
ggplot(host_competence.gg.heat.s.p) +
geom_point(aes(est, host), lwd = 0.5) +
geom_errorbarh(aes(xmin = lwr, xmax = upr, y = host), height = 0.5, lwd = 0.30, linetype = "solid") +
scale_x_continuous(breaks = c(0, 1.5, 3.0), labels = c("0.0", "1.5", "3.0")) +
theme(
panel.grid = element_blank()
, legend.key.size = unit(.65, "cm")
, legend.title = element_text(size = 12)
, legend.text = element_text(size = 10)
, panel.border = element_rect(colour = "black", fill = NA, size = 0)
, axis.line = element_line()
, axis.text.y = element_text(size = 10)
, axis.text.x = element_text(size = 8)
, axis.title.x = element_text(size = 10)
, axis.title.y = element_text(size = 12)
) +
xlab("Total Host to
Mosquito
Infections") + ylab("")
ggsave(filename = "/Users/Morgan/Desktop/host_B1.pdf", plot = last_plot(), width = 1.8, height = 2.5, units = c("in"))
## The matrix part of the panel
ggplot(host_competence.mat.gg.s
, aes(mosq, host)) +
geom_tile(aes(fill = est)
, colour = "white") +
scale_fill_gradient(low = "grey95", high = "#4472C4"
, name = "Infected
mosquitoes") +
theme(
axis.text.x = element_text(angle = 300, hjust = 0, colour = "grey50", size = 9)
, legend.key.size = unit(.35, "cm")
, legend.text = element_text(size = 9)
, legend.title = element_text(size = 10)
, axis.text.y = element_text(size = 0)
, axis.title.x = element_text(size = 10)
, axis.title.y = element_text(size = 10)
) +
ylab("") +
xlab("Newly Infected Mosquitoes")
ggsave(filename = "/Users/Morgan/Desktop/host_B2.pdf", plot = last_plot(), width = 2.65, height = 3.13, units = c("in"))
####
## Mosquito panel 2, Mosquito to Host transmission matrix and summary CI plot
####
ggplot(m_to_h_mat.gg.s) +
geom_point(aes(est, mosq), lwd = 0.5) +
geom_errorbarh(aes(xmin = lwr, xmax = upr, y = mosq), height = 0.5, lwd = 0.3) +
theme(
panel.grid = element_blank()
, legend.key.size = unit(.65, "cm")
, legend.title = element_text(size = 12)
, legend.text = element_text(size = 10)
, panel.border = element_rect(colour = "black", fill = NA, size = 0)
, axis.line = element_line()
, axis.text.y = element_text(size = 8)
, axis.text.x = element_text(size = 10)
, axis.title.x = element_text(size = 10)
, axis.title.y = element_text(size = 12)
) +
xlab("Total Mosquito
to Host
Infections") +
ylab("") + scale_x_continuous(lim = c(0, 3), breaks = c(0, 1, 2, 3))
ggsave(filename = "/Users/Morgan/Desktop/mosq_B1.pdf", plot = last_plot(), width = 2.15, height = 2.5, units = c("in"))
## Matrix component
ggplot(m_to_h_mat.gg.mh
, aes(host, mosq)) +
geom_tile(aes(fill = est)
, colour = "white") +
scale_fill_gradient(low = "grey95", high = "orangered4"
, breaks = c(0.40, 0.70, 1.00, 1.30)
, labels = c(0.40, 0.70, 1.00, 1.30)
, name = "Infected
hosts") +
theme(
axis.text.x = element_text(angle = 300, hjust = 0, colour = "grey50", size = 9)
, legend.key.size = unit(.35, "cm")
, legend.text = element_text(size = 8)
, legend.title = element_text(size = 8)
, axis.text.y = element_text(size = 0)
, axis.title.x = element_text(size = 10)
, axis.title.y = element_text(size = 10)
) +
ylab("") +
xlab("Newly Infected Hosts")
ggsave(filename = "/Users/Morgan/Desktop/mosq_B2.pdf", plot = last_plot(), width = 3.2, height = 2.62, units = c("in"))
####
## Host Panel 3, Host to Host transmission matrix and summary CI plot
####
## NOTE: for the supplemental "exposure" figure (currently Supplemental figure) use:
## physiol_mat.s.all.gg.supp
## physiol_mat.gg.f.p.supp
## Summary panel components
ggplot(
# physiol_mat.s.all.gg
physiol_mat.s.all.gg.supp
, aes(est_tot, G1)) +
geom_point(lwd = 0.5) +
geom_errorbarh(aes(xmin = lwr_tot, xmax = upr_tot, y = G1), height = 0.5, lwd = 0.3) +
# scale_x_continuous(breaks = c(0, 1.5, 3.0, 4.5, 6.0), labels = c("0.0", "1.5", "3.0", "4.5", "6.0")) +
scale_x_continuous(breaks = c(0, 1.0, 2.0), labels = c("0.0", "1.0", "2.0"), lim = c(0, 2)) +
ylab("") +
xlab("Total Host to
Host Infections") +
theme(
panel.grid = element_blank()
, legend.key.size = unit(.35, "cm")
, legend.title = element_text(size = 12)
, legend.text = element_text(size = 10)
, panel.border = element_rect(colour = "black", fill = NA, size = 0)
, axis.line = element_line()
, axis.text.y = element_text(size = 10)
, axis.text.x = element_text(size = 8)
, axis.title.x = element_text(size = 10)
, axis.title.y = element_text(size = 12)
)
ggsave(filename = "/Users/Morgan/Desktop/host_C1.pdf", plot = last_plot(), width = 1.8, height = 2.35, units = c("in"))
ggplot(
# physiol_mat.s.all.gg
physiol_mat.s.all.gg.supp
, aes(est_prop, G1)) +
geom_point(lwd = 0.5) +
scale_x_continuous(breaks = c(0, 0.3, 0.6, 0.9), labels = c("0", "0.3", "0.6", "0.9"), lim = c(0, 0.9)) +
geom_errorbarh(aes(xmin = lwr_prop, xmax = upr_prop, y = G1), height = 0.5, lwd = 0.3) +
ylab("") +
xlab("Proportion of
Infections Self") +
theme(
panel.grid = element_blank()
, legend.key.size = unit(.65, "cm")
, legend.title = element_text(size = 12)
, legend.text = element_text(size = 10)
, panel.border = element_rect(colour = "black", fill = NA, size = 0)
, axis.line = element_line()
, axis.text.y = element_text(size = 10)
, axis.text.x = element_text(size = 10)
, axis.title.x = element_text(size = 10)
, axis.title.y = element_text(size = 12)
)
ggsave(filename = "/Users/Morgan/Desktop/host_C2.pdf", plot = last_plot(), width = 1.8, height = 2.35, units = c("in"))
## Matrix panel component
ggplot(
# physiol_mat.gg.f.p
physiol_mat.gg.f.p.supp
, aes(G2, G1)) +
geom_tile(aes(fill = comp.est)
, colour = "white") +
scale_fill_gradient(low = "grey95", high = "#4472C4"
, name = "Second
generation
hosts
exposed
per host") +
theme(
axis.text.x = element_text(angle = 300, hjust = 0, colour = "grey50", size = 9)
, legend.key.size = unit(.45, "cm")
, legend.text = element_text(size = 10)
, legend.title = element_text(size = 10)
, axis.text.y = element_text(size = 0)
, axis.title.x = element_text(size = 10)
, axis.title.y = element_text(size = 10)
) +
ylab("") +
xlab("Second Generation Host")
ggsave(filename = "/Users/Morgan/Desktop/host_C3.pdf", plot = last_plot(), width = 3.00, height = 2.65, units = c("in"))
####
## Mosquito Panel 3, mosquito to mosquito transmission matrix and summary CI plot
####
## Summary panel component
ggplot(physiol_mat.s.all.gg.mm, aes(est_tot, G1)) +
geom_point(lwd = 0.5) +
geom_errorbarh(aes(xmin = lwr_tot, xmax = upr_tot, y = G1), height = 0.5, lwd = 0.3) +
ylab("") +
xlab("Total Mosquito
to Mosquito
Infections") +
theme(
panel.grid = element_blank()
, legend.key.size = unit(.65, "cm")
, legend.title = element_text(size = 12)
, legend.text = element_text(size = 10)
, panel.border = element_rect(colour = "black", fill = NA, size = 0)
, axis.line = element_line()
, axis.text.y = element_text(size = 8)
, axis.text.x = element_text(size = 10)
, axis.title.x = element_text(size = 10)
, axis.title.y = element_text(size = 12)
) + scale_x_continuous(breaks = c(0, 1.5, 3))
ggsave(filename = "/Users/Morgan/Desktop/mosq_C1.pdf", plot = last_plot(), width = 2.2, height = 2.50, units = c("in"))
ggplot(physiol_mat.s.all.gg.mm, aes(est_prop, G1)) +
geom_point(lwd = 0.5) +
geom_errorbarh(aes(xmin = lwr_prop, xmax = upr_prop, y = G1), height = 0.5, lwd = 0.3) +
ylab("") +
xlab("Proportion of
Infections Self") +
theme(
panel.grid = element_blank()
, legend.key.size = unit(.65, "cm")
, legend.title = element_text(size = 12)
, legend.text = element_text(size = 10)
, panel.border = element_rect(colour = "black", fill = NA, size = 0)
, axis.line = element_line()
, axis.text.y = element_blank()
, axis.text.x = element_text(size = 10)
, axis.title.x = element_text(size = 10)
, axis.title.y = element_text(size = 12)
) + scale_x_continuous(lim = c(0, 1.0), breaks = c(0.0, 0.5, 1.0))
ggsave(filename = "/Users/Morgan/Desktop/mosq_C2.pdf", plot = last_plot(), width = 1.15, height = 2.34, units = c("in"))
## Matrix panel component
ggplot(physiol_mat.gg.f.p.mm
, aes(G2, G1)) +
geom_tile(aes(fill = comp.est)
, colour = "white") +
scale_fill_gradient(low = "grey95", high = "orangered4"
, breaks = c(0.0, 0.15, 0.30, 0.45)
, labels = c(0.0, 0.15, 0.30, 0.45)
, lim = c(0, 0.55)
, name = "Second
generation
mosquitoes
infected
per mosquito") +
theme(
axis.text.x = element_text(angle = 300, hjust = 0, colour = "grey50", size = 8)
, legend.key.size = unit(.35, "cm")
, legend.text = element_text(size = 8)
, legend.title = element_text(size = 8)
, axis.text.y = element_blank()
, axis.title.x = element_text(size = 10)
, axis.title.y = element_text(size = 10)
) +
ylab("") +
xlab("Second Generation Mosquito")
ggsave(filename = "/Users/Morgan/Desktop/mosq_C3.pdf", plot = last_plot(), width = 3.1, height = 2.99, units = c("in"))
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