magreport.Rmd

---
title: "Dynamics of within-species Variation"
subtitle: "`r paste0('Genome: ', cur_genome, '. Taxonomy: ', tax_df$Tax)`"
author: "Giulio Benedetti"
date: "`r Sys.Date()`"
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(fig.path = paste0("results/", cur_genome, "_"),
                      echo = FALSE)
```

```{r polyline, fig.height = 10, fig.width = 20}
p <- (p2 / p3 | p1) +
    plot_layout(guides = "collect")
p
```

```{r polymap, fig.height = 15, fig.width = 15}
draw(Heatmap(count_mat,
             name = "SPS Percent",
             heatmap_legend_param = list(at = seq(0, 1, by = 0.2)),
             col = col_fun,
             cluster_rows = FALSE,
             cluster_columns = FALSE,
             row_title = "Reference Sample",
             column_title = "Observed Sample",
             column_names_rot = 90,
             left_annotation = row_ha,
             bottom_annotation = col_ha_bottom,
             top_annotation = col_ha_top,
             show_row_names = FALSE,
             show_column_names = FALSE),
     annotation_legend_list = list(lgd_gvalue, lgd_sig))
```