11_AssembleFigures.qmd

---
title: "Create figures for manuscript"
author: Jamie Soul
format:
  html:
    self-contained: true
    theme: litera
    toc: true
editor: visual
code-block-bg: true
code-block-border-left: "#31BAE9"
---

# Combined saved figures for publication

## Load libraries

```{r}
#| output: false
library(ggplot2)
library(patchwork)
library(ComplexHeatmap)
library(cowplot)
library(grid)
library(gridExtra)
library(GeomxTools)
library(GeoMxWorkflows)
library(ggsci)
library(tidyverse)

```

## Figure 2

### Load the saved figures

```{r}
pca <- readRDS("results/Fig2A_PCA.RDS")
pca2 <- readRDS("results/Fig2B_PCA.RDS")

#Alter the text labels in the legend
pca <- pca  + scale_color_npg(labels = c("CD45" = expression(CD45^"+"),"CD56"=expression(CD56^"+"),"PANCK"=expression(PanCK^"+")))

pca2 <- pca2  + scale_color_npg(labels = c("CD45" = expression(CD45^"+"),"CD56"=expression(CD56^"+"),"PANCK"=expression(PanCK^"+")))

heatmap <- readRDS("results/Fig2B_Heatmap.RDS")
heatmap <- grid.grabExpr(draw(heatmap)) 

deconv <- readRDS("results/Fig2C_spatialDeconBroadHeatmap.RDS")
deconv <- grid.grabExpr(draw(deconv)) 
i <- grep("text",names(deconv$children))

for (j in i) {
  deconv$children[[j]]$gp$fontsize <- 14
  
}
```

### Assemble figure 2

```{r}
fig2 <- (pca + pca2)/deconv/ heatmap + 
  plot_layout(widths = c(1,1,2),heights = c(1,0.9,2)) +
  plot_annotation(tag_levels = 'A') & 
  theme_cowplot() & 
  theme(plot.tag = element_text(face = 'bold',size = 18))

save_plot(filename ="figures/Fig2.pdf",fig2,base_height = 11,base_width = 8, bg="white")
```

## Figure 3

### Load the saved figures

```{r}
heatmaps <- readRDS("results/Fig3B_Heatmap.RDS")
target_spatialData <- readRDS("results/normalisedSpatialData.RDS")
regions <- unique(pData(target_spatialData)$Region)[1:6]
regions <- gsub("Control ","",regions)

names(regions) <- c("Luminal epithelium",
                    "Sub-luminal stromal CD45+",
                    "Sub-luminal stroma",
                    "Glandular epithelium",
                    "Functionalis stromal CD56+",
                    "Functionalis stroma")

heatmaps <- mapply(function(heatmap,title){
  heatmap@column_title <- title
  heatmap
},heatmaps,names(regions))

names(heatmaps) <- names(regions)
heatmaps <- heatmaps[c("Luminal epithelium",
                       "Glandular epithelium",
                       "Sub-luminal stroma",
                       "Functionalis stroma",
                       "Sub-luminal stromal CD45+",
                       "Functionalis stromal CD56+")]


```

```{r}

heatmaps <- lapply(heatmaps,function(x) grid.grabExpr(draw(x)) )


# Arrange the heatmaps in a grid layout
g <- grid.arrange(
    arrangeGrob(heatmaps$`Luminal epithelium`, top = textGrob("A", x = unit(0, "npc"), y = unit(1, "npc"), just = c("left", "top"), gp = gpar(fontsize = 30, fontface = "bold"))),
    arrangeGrob(heatmaps$`Glandular epithelium`, top = textGrob("B", x = unit(0, "npc"), y = unit(1, "npc"), just = c("left", "top"), gp = gpar(fontsize = 30, fontface = "bold"))),
    arrangeGrob(heatmaps$`Sub-luminal stroma`, top = textGrob("C", x = unit(0, "npc"), y = unit(1, "npc"), just = c("left", "top"), gp = gpar(fontsize = 30, fontface = "bold"))),
    arrangeGrob(heatmaps$`Functionalis stroma`, top = textGrob("D", x = unit(0, "npc"), y = unit(1, "npc"), just = c("left", "top"), gp = gpar(fontsize = 30, fontface = "bold"))),
    arrangeGrob(heatmaps$`Sub-luminal stromal CD45+`, top = textGrob("E", x = unit(0, "npc"), y = unit(1, "npc"), just = c("left", "top"), gp = gpar(fontsize = 30, fontface = "bold"))),
    arrangeGrob(heatmaps$`Functionalis stromal CD56+`, top = textGrob("F", x = unit(0, "npc"), y = unit(1, "npc"), just = c("left", "top"), gp = gpar(fontsize = 30, fontface = "bold"))),
    ncol = 2
)

save_plot("figures/Fig3.pdf",g,base_height = 16,base_width = 12)
```

### Figure 3 VolcanoPlots

```{r}
volcanoplots <- readRDS("results/diseaseVolcanoPlots.RDS")

volcanoplots <- volcanoplots[c(5,2,6,3,4,1)]
names(volcanoplots) <- c("Luminal epithelium","Glandular epithelium","Sub-luminal stroma","Functionalis stroma","Sub-luminal stromal CD45+","Functionalis stromal CD56+")

volcanoplots <- mapply(function(x,y){
  x <- x + ggtitle(y)
  x
},volcanoplots,names(volcanoplots),SIMPLIFY = FALSE)


volcanoplots <- volcanoplots %>%
  plot_grid(plotlist = . ,ncol = 2,labels = "AUTO",label_size = 20)


save_plot(plot = volcanoplots, filename = "figures/Fig3.pdf",base_height = 16,base_width = 10,bg="white")


```

## Figure 4

### Load the saved figures

```{r}
enrichmentPlots <- readRDS("results/enrichmentPlots.RDS")

goPlot <- enrichmentPlots[[1]] + scale_x_discrete(labels=c("Functionalis stromal CD56+",
"Glandular epithelium",
"Functionalis stroma",
"Sub-luminal stromal CD45+",
"Luminal epithelium",
"Sub-luminal stroma"))
keggPlot <-  enrichmentPlots[[2]] + scale_x_discrete(labels=c("Functionalis stromal CD56+",
"Glandular epithelium",
"Functionalis stroma",
"Sub-luminal stromal CD45+",
"Luminal epithelium",
"Sub-luminal stroma"))

```

### Assemble figure 4

```{r}
fig4 <-  (goPlot + keggPlot) +
  plot_annotation(tag_levels = 'A')  & 
  theme(plot.tag = element_text(face = 'bold',size = 24))

save_plot(filename ="figures/Fig4.pdf",fig4,base_height = 9,base_width = 16, bg="white")
```

### Supplementary Figures

```{r}
file.copy("figures/Normalisation/antibodyValues.pdf","figures/SupplementryFigure1.pdf")
```

### Supplementary tables

```{r}


file.copy("results/diffExpLME4_betweenCells.xlsx","tables/SupplementryTable1.xlsx")

file.copy("results/cellTypeGeneOntology.xlsx","tables/SupplementryTable2.xlsx")


file.copy("results/diffExpLME4_Q3.xlsx","tables/SupplementryTable3.xlsx")

file.copy("results/diseasePathways.xlsx","tables/SupplementryTable5.xlsx")

file.copy("results/diseaseGeneOntology.xlsx","tables/SupplementryTable6.xlsx")

file.copy("results/signatureSearch_Touchstone.xlsx","tables/SupplementryTable7.xlsx")

file.copy("results/drugTargetEnrichment.xlsx","tables/SupplementryTable8.xlsx")

```