Landscapes.Rmd

---
title: "Landscapes"
author: "Matt Nolan"
date: "26/03/2019"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
set.seed(1)
```




```{r, warning=FALSE}
landscape <- tibble(x = seq(0, 20, length=1000), y = dnorm(x, mean=10, sd=3) * -1, cell = rbinom(n = length(x), size = 1, prob = (y^8/min(y)^8)/25))
(landscape_plot <- ggplot(landscape, aes(x,y)) +
  geom_line() +
  geom_point(aes(size = ifelse(cell==0, NA, cell))) +
  theme_void() +
  theme(legend.position="none"))

(landscape_plot_2 <- landscape_plot +
  geom_segment(aes(x = 10,y = -0.152,xend = 10,yend = -0.142), arrow = arrow(length = unit(0.1, "inches"))) +
  draw_label("Fixed set point", 5, 0.01) +
  ylim(-0.16,0.02))

(landscape_plot_3 <- landscape_plot +
  geom_segment(aes(x = 10, y = -0.162,xend = 10,yend = -0.147), arrow = arrow(length = unit(0.1, "inches"))) +
  ylim(-0.18,0.02))
```


```{r, warning=FALSE}
landscapes <- tibble(x = seq(0, 30, length=3000),
                     y1 = dnorm(x, mean=10, sd=3) * -1,
                     cell1 = rbinom(n = length(x), size = 1, prob = (y1^8/min(y1)^8)/25),
                     y2 = dnorm(x, mean=20, sd=3) * -1,
                     cell2 = rbinom(n = length(x), size = 1, prob = (y2^8/min(y2)^8)/25))

(landscapes_plot <- ggplot(landscapes) +
  geom_line(aes(x, y1)) +
  geom_point(aes(x, y1, size = ifelse(cell1==0, NA, cell1)), shape = 5) +
  geom_line(aes(x,y2)) +
  geom_point(aes(x, y2, size = ifelse(cell2==0, NA, cell2)), shape = 6) +
  theme_void() +
  theme(legend.position="none"))

(landscapes_plot_2 <- landscapes_plot +
  geom_segment(aes(x = 10,y = -0.152,xend = 10,yend = -0.142), arrow = arrow(length = unit(0.1, "inches"))) +
  geom_segment(aes(x = 20,y = -0.152,xend = 20,yend = -0.142), arrow = arrow(length = unit(0.1, "inches"))) +
  draw_label("Variable set point", 10, 0.01) +
  ylim(-0.16,0.02))

(landscapes_plot_3 <- landscapes_plot +
  geom_segment(aes(x = 10,y = -0.167,xend = 10,yend = -0.152), arrow = arrow(length = unit(0.1, "inches"))) +
  geom_segment(aes(x = 20,y = -0.167,xend = 20,yend = -0.152), arrow = arrow(length = unit(0.1, "inches"))) +
  draw_label("Variable", 10, 0.02) +
  ylim(-0.18,0.02))

num_reps = 10
seq_length = 3000
landscapes_multiple <- tibble(x = rep(seq(0, 30, length=seq_length), num_reps),
                              reps =  rep(1:num_reps, each = seq_length),
                              reps_fac = as.factor(reps),
                              y = dnorm(x, mean=9 + reps, sd=3) * -1,
                              cell = rbinom(n = seq_length * num_reps, size = 1, prob = (y^8/min(y)^8)/25))

(landscapes_m_plot <- ggplot() +
  geom_line(data = landscapes_multiple, aes(x,y, colour = reps_fac)) +
    #scale_colour_brewer(direction = -1)
    scale_colour_hue(h = c(180,270))
)

arrow_coords <- tibble(x = c(9 + 1:num_reps), y = c(rep(-0.152, num_reps)), xend = c(9 + 1:num_reps), yend = c(rep(-0.137, num_reps)))

(landscapes_m_plot_2 <- landscapes_m_plot +
  geom_segment(data = arrow_coords, aes(x = x, y = y, xend = xend, yend = yend), arrow = arrow(length = unit(0.1, "inches"))) +
  theme_void() +
  theme(legend.position="none") +
  ylim(-0.18,0.02))
```

```{r, warning=FALSE}
ggdraw() +
  draw_plot(landscape_plot, 0.05, 0, 0.4, 0.9) +
  draw_plot(landscapes_plot, 0.55, 0, 0.4, 0.9) +
  draw_plot_label(c("A", "B"), c(0, 0.5), c(1,1), size = 24) +
  draw_plot_label(c("Fixed set point", "Variable set point"), c(0.05, 0.5), c(0.98,0.98), size = 18)
```

```{r, warning=FALSE}
ggdraw() +
  draw_plot(landscape_plot_2, 0.05, 0, 0.4, 1) +
  draw_plot(landscapes_plot_2, 0.55, 0, 0.4, 1) +
  draw_plot_label(c("A", "B"), c(0, 0.5), c(0.97,0.97), size = 24)
```


```{r, warning=FALSE}
num_cells <- 4
length_plot <- 6000
landscapes_4  <- tibble(x = rep(seq(0, 60, length=length_plot), num_cells),
                        setpoint_pos = c(rep(10, length_plot), rep(20, length_plot), rep(25, length_plot), rep(50, length_plot)),
                        y = dnorm(x, mean=setpoint_pos, sd=3) * -1,
                        cell_prob = rbinom(n = length(x), size = 1, prob = y^2))

ggplot(landscapes_4) + geom_line(aes(x, y, colour = as.factor(setpoint_pos))) +
  geom_point(aes(x, y, size = ifelse(cell_prob==0, NA, cell_prob), colour = as.factor(setpoint_pos))) +
  theme_void() +
  theme(legend.position="none")

```

```{r}
dvplot <- function(tb, ylabel = "Gradient factor", line_palette = "Reds") {
  ggplot(tb) +
  geom_segment(aes(x = x, y = y, xend = xend, yend = yend, colour = group)) +
  xlim(0,1) +
  ylim(0,1) +
  xlab("Location") +
  ylab (ylabel) +
  theme(axis.text=element_blank(),
        axis.ticks=element_blank(),
        legend.position = "none")  +
  scale_colour_brewer(type = "seq", palette = line_palette)
}


num_cases <- 15
slope_lines <- tibble(x = rep(0,num_cases),
                      y = rep(1,num_cases),
                      xend = rep(1,num_cases),
                      yend = seq(0.2, 0.8, length.out = num_cases),
                      group = as.factor(1:num_cases))
(sl_plot <- dvplot(slope_lines))

h_lines <- tibble(x = rep(0,num_cases),
                  y = seq(0.2, 0.6, length.out = num_cases),
                  xend = rep(1,num_cases),
                  yend = seq(0.2, 0.6, length.out = num_cases),
                  group = as.factor(1:num_cases))
(h_plot <- dvplot(h_lines, "Unifrom factor", "Blues"))

setpoint <- tibble(x = rep(0,num_cases),
                   y = runif(num_cases, 0.6, 1),
                   xend = rep(1,num_cases),
                   yend = runif(num_cases, 0.2, 0.6),
                   group = as.factor(1:num_cases))
(sp_plot <- dvplot(setpoint, "Set point", "Greens"))

```

```{r}
ggdraw() +
  draw_plot(landscape_plot_2, 0.05, 0.5, 0.3, 0.5) +
  draw_plot(landscapes_plot_2, 0.05, 0, 0.3, 0.5) +
  draw_plot(sl_plot, 0.45, 0.5, 0.25, 0.4) +
  draw_plot(h_plot, 0.45, 0, 0.25, 0.4) +
  draw_plot(sp_plot, 0.75, 0.25, 0.25, 0.4) +
  draw_plot_label(c("A", "B" ,"C", "X"), c(0, 0, 0.42, 0.7), c(1,0.5, 1, 0.5), size = c(24,24,24,18))

```



```{r}
ggsave("Figures/Landscape_figure.png", width = 220, height = 140, units = "mm")
```