figures.qmd

---
geometry: "margin=2.5cm"
output:
  pdf_document:
    toc: no
    number_sections: no
header-includes:
  - \pagenumbering{gobble}
mainfont: Arial
---

```{r echo = FALSE}

knitr::opts_chunk$set(
  echo = FALSE,
  include = TRUE,
  warning = FALSE,
  message = FALSE,
  error = FALSE
)


```


```{r setup_figs}

source("src/libs.R")
library(magick)
circos_cols <- readRDS("data/circos_colours.RDS")

make_title <- function(text){
  ggdraw() +
  draw_label(
    text,
    fontface = 'bold',
    x = 0,
    hjust = 0,
    size = 22
  ) +
  theme(
    # add margin on the left of the drawing canvas,
    # so title is aligned with left edge of first plot
    plot.margin = margin(0, 0, 0, 7)
  )
}

```


```{r}
#| label: fig-1
#| fig-width: 14
#| fig-height: 10
#| out-width: 100%
#| out-height: 100%

response <- readRDS("figures/response_barplot.RDS")
bmt <- readRDS("figures/bmt_barplot.RDS")

legend1 <- cowplot::get_legend(
  response +
  theme(
    legend.position = "right",
    legend.direction = "vertical"
  ) +
  guides(fill = "none")
)
legend2 <- cowplot::get_legend(
  response +
  theme(
    legend.position = "right",
    legend.direction = "vertical"
  ) +
  guides(alpha = "none")
)

legends <- plot_grid(
  legend1,
  legend2,
  NULL,
  nrow = 1
)

barplots <- plot_grid(
  response + theme(legend.position = "none"),
  legends,
  bmt + ylab("Received \nHSCT (%)"),
  ncol = 1,
  rel_heights = c(1, 0.5, 1),
  labels = c("A", "",  "B"),
  label_size = 22,
  align = "hv",
  axis = "l"
)
# barplots <- plot_grid(
#   barplots,
#   legends,
#   ncol = 2,
#   rel_widths = c(1, 1)
# )

# surv <- image_read_pdf("figures/surv_with_tables_edited.pdf", density = 150)
# surv <- image_ggplot(surv)

surv <- readRDS("figures/surv_with_tables.RDS")


pre_fig1 <- plot_grid(
  barplots,
  surv,
  nrow = 1,
  rel_widths = c(1, 2.4)
)

fig1_title <- make_title("")

fig1 <- plot_grid(
  fig1_title,
  pre_fig1,
  ncol = 1,
  rel_heights = c(0.1, 2)
)

fig1

```

```{r}
#| label: fig-2
#| fig-width: 11
#| fig-height: 13
#| out-width: \\linewidth
#| fig-align: center
#|

swimmer <- image_read_pdf("./figures/swimmer_plot_breaks_edited.pdf",
density = 300)
swimmer <- image_ggplot(swimmer, interpolate = TRUE)



title <- make_title("")


fig2 <- plot_grid(
  title,
  swimmer,
  nrow = 3,
  rel_heights = c(0.05, 1)
)

fig2


```


\newpage

```{r}
#| label: fig-3
#| fig-width: 12
#| fig-height: 14
#| out-width: 100%
#| out-height: 100%
#| fig-align: center

total_vs_shared <- readRDS("figures/shared_vs_total.RDS")
unique_vs_time <- readRDS("figures/percent_unique_linear.RDS")

fig3_ab <- plot_grid(
  total_vs_shared,
  unique_vs_time + theme(legend.position = "none"),
  ncol = 1,
  labels = c("C", "D"),
  label_size = 22
)

oncoplots <- paste0(
  "figures/oncoplot_",
  c("Diagnosis", "Shared", "Relapse"),
  ".pdf"
)
oncoplot_list <- lapply(
  oncoplots,
  function(x){
    oncoplot <- image_read_pdf(x)
    oncoplot <- image_ggplot(oncoplot, interpolate = TRUE)
    return(oncoplot)
  }
)

oncoplots_arranged <- plot_grid(
  oncoplot_list[[1]],
  oncoplot_list[[2]],
  oncoplot_list[[3]],
  nrow = 1
)

mixcr_igh <- readRDS("figures/mixcr_heavychain_alluvial.RDS")
mixcr_lc <- readRDS("figures/mixcr_lightchain_alluvial.RDS")

fig_3de <- plot_grid(
  plot_grid(NULL, mixcr_igh, NULL, rel_widths = c(0.1, 1, 0.1), nrow = 1),
  plot_grid(NULL, mixcr_lc, NULL, rel_widths = c(0.1, 1, 0.1), nrow = 1),
  nrow = 2,
  labels = c("D", "E"),
  label_size = 22,
  align = "hv",
  axis = "l"
)

pre_fig3 <- plot_grid(
  fig3_ab,
  fig_3de,
  ncol = 1,
  rel_heights = c(1.3, 1)
)

title3 <- make_title("")

fig3 <- plot_grid(
  title3,
  pre_fig3,
  label_size = 22,
  rel_heights = c(0.05, 1),
  ncol = 1
)

fig3

```


```{r}
#| label: fig-4
#| fig-width: 22
#| fig-height: 10
#| out-width: 100%
#| out-height: 100%
#| fig-align: center

panel_4a <- readRDS("./figures/fish_pairs.RDS")
panel_4a <- panel_4a +
  ylab("Count")

diagnosis_cols <- c("#388697", "#FC5130")
names(diagnosis_cols) <- c("Diagnosis", "Relapse")


svcircos1 <- image_read_pdf("./figures/03-23488-IG-MYC.pdf", density = 300)
svcircos1 <- image_ggplot(svcircos1, interpolate = TRUE)
svcircos1 <- svcircos1 +
  annotate("text",
           x = c(250, 1000),
           y = 150,
           label = c("Diagnosis", "Relapse"),
           size = 5,
           fontface = 2,
           colour = diagnosis_cols)

svcircos2 <- image_read_pdf("./figures/07-25994-IG-MYC.pdf", density = 300)
svcircos2 <- image_ggplot(svcircos2, interpolate = TRUE)
svcircos2 <- svcircos2 +
  annotate("text",
           x = c(250, 1000),
           y = 150,
           label = c("Relapse", "Diagnosis"),
           size = 5,
           fontface = 2,
           colour = diagnosis_cols[c("Relapse", "Diagnosis")])

svpanel <- plot_grid(svcircos1, svcircos2, nrow = 2, label_size = 22)



panel_4a_b <- plot_grid(
  panel_4a,
  svpanel,
  nrow = 1,
  labels = c("A", "B"),
  rel_widths = c(1.8, 1),
  label_size = 22
)

coo_alluvial <- readRDS("figures/coo_alluvial.RDS")
coo_score <- readRDS("figures/coo_score.RDS")

coo_legend <- get_legend(
  coo_alluvial +
    theme(
      legend.position = c(0.35, 0),
      legend.direction = "horizontal",
      legend.margin = margin(0,0,40,0)
    )
)

coo_score <- coo_score + theme(panel.spacing = unit(2, "lines"))

lg_panel <- readRDS("figures/lymphgen_comparison.RDS")
lg_panel <- lg_panel +
  ylab("Count") +
  theme(legend.position = "bottom",
        legend.direction = "horizontal")

# shared_muts_panel <- readRDS("figures/percent_unique_boxplot_wide.RDS")

fig4_title <- make_title("")

panel_4cde <- plot_grid(
  coo_alluvial + theme(legend.position = "none"),
  coo_legend,
  coo_score,
  lg_panel,
  # shared_muts_panel,
  labels = c("C", "", "D", "E"),
  ncol = 1,
  rel_heights = c(1, 0.1, 1, 1.2),
  label_size = 22,
  align = "v",
  axis = "l"
)

fig4 <- plot_grid(
  panel_4a_b,
  panel_4cde,
  rel_widths = c(1.5,1),
  ncol = 2
)

fig4

```

\newpage

```{r}
#| label: fig-5
#| fig-width: 10
#| fig-height: 12
#| out-width: 100%
#| out-height: 100%

patients <- c(
  "16-27074",
  "14-20552",
  "01-14774",
  "03-23488",
  "06-11677"
)

plot_dir <- "figures/phyclone_plots_lymphgen_lst_callable_indels/"

plot_list <- lapply(
  patients,
  function(x){
    loaded <- image_read_pdf(dir(plot_dir, pattern = x, full.names = TRUE))
    ggplot <- image_ggplot(loaded, interpolate = TRUE)
    return(ggplot)
  }
)

fig5_title <- make_title("")

pre_fig5 <- plot_grid(
  plotlist = plot_list,
  ncol = 1,
  labels = c(
    "A", "B", "C", "D", "E"
  ),
  label_size = 22
)

plot_grid(
  fig5_title,
  pre_fig5,
  ncol = 1,
  rel_heights = c(0.05, 1)
)

```

\newpage

```{r}
#| label: fig-6
#| fig-width: 15
#| fig-height: 11
#| out-width: 100%
#| out-height: 100%


trunk_vs_unique <- readRDS("figures/clonal_features.RDS") +
scale_y_continuous(breaks = scales::breaks_pretty(2))
constrained <- readRDS("figures/constrained_features.RDS")+
scale_y_continuous(breaks = scales::breaks_pretty(2))

panel_6ab <- plot_grid(
  trunk_vs_unique,
  constrained,
  ncol = 1,
  labels = c("A", "B"),
  label_size = 22
)

lowgrade <- readRDS("figures/lg_vs_lowgrade_entity.RDS")
lowgrade <- lowgrade +
theme(legend.position = c(0.75, 0.75))

model <- image_read_pdf("figures/DLBCL Evolution Model.pdf", density = 150)
model <- image_ggplot(model, interpolate = TRUE)

panel_6cd <- plot_grid(
  lowgrade,
  plot_grid(NULL, model, NULL, rel_widths = c(0.1, 1, 0.1), nrow = 1),
  ncol = 1,
  labels = c("C", "D"),
  label_size = 22
)

pre_fig6 <- plot_grid(
  panel_6ab,
  panel_6cd,
  nrow = 1,
  rel_widths = c(1, 0.8)
)

title6 <- make_title("")

fig6 <- plot_grid(
  title6,
  pre_fig6,
  ncol = 1,
  rel_heights = c(0.05, 1)
)

fig6

```