report_template.Rmd

---
output:
  pdf_document:
    latex_engine: xelatex
header-includes:
    - \usepackage{fancyhdr}
    - \usepackage{fontspec}
    - \usepackage{xcolor}
    - \geometry{left = 0.5in,right = 0.5in}
mainfont: Roboto
sansfont: Roboto
urlcolor: purplepeopleeater
---
<!-- define color and adjust lengths for header and footer-->
\definecolor{purplepeopleeater}{RGB}{106,13,75}
\definecolor{darkestnight}{RGB}{0,0,0}
\addtolength{\headheight}{3.0cm}
\addtolength{\topmargin}{-0.5in}
\addtolength{\footskip}{-0.225in}

<!-- % setup header -->
\pagestyle{fancy}
\fancyhf{}

<!-- header content -->
<!-- Uncomment the line of code below to include a header -->
<!-- \fancyhead[L]{\raisebox{-0.25\height}{\includegraphics[height = 2.5cm]{path_to_your_header_here.png}}} -->
\fancyhead[R]{\Huge Genomic Clustering Report\\
\Large `r paste(Sys.Date())`}

<!-- create red header line -->
\renewcommand{\headrulewidth}{1pt}
\renewcommand{\headrule}{\hbox to\headwidth{%
    \color{darkestnight}\leaders\hrule height \headrulewidth\hfill}}

<!-- footer content -->
\fancyfoot[C]{For research use only, not for clinical use.}
\fancyfoot[R]{\thepage}

<!-- create red footer line -->
\renewcommand{\footrulewidth}{1pt}
\renewcommand{\footrule}{\hbox to\headwidth{%
    \color{darkestnight}\leaders\hrule height \headrulewidth\hfill}}

```{r include=FALSE}

## Libraries
library(ggplot2)
library(ggtree)
library(phytools)
library(viridisLite)
library(viridis)
library(tidyverse)

date <- Sys.Date()

## Figure size

# get date of report generation
date <- Sys.Date()

# set figure size
knitr::opts_chunk$set(out.width = "7.5in", out.height = "8in", fig.align = "left")

# set seed for reproducibility
set.seed(123)



```

```{r heatmap-ploting-defaults, echo = FALSE, message = FALSE, warning = FALSE}

# alter these plotting defaults as necessary

# heatmap width relative to plot
heatmap_width <- 30

# font size for heatmap row and column names
axis_font_size <- 2.25

# font size for heatmap values
cell_font_size <- 2.25

# tree offset from heatmap
tree_offset <- 50

# offset of column names from heatmap; should be negative
col_offset <- -2

# offset of row names names from heatmap
row_offset <- -40

# legend title font size
legend_title_size <- 8

# legend body font size
legend_text_size <- 6

# height of heatmap colourbar
colourbar_height <- 0.5

# width of heatmap colourbar
colourbar_width <- 7

```

```{r tree-plot-defaults, echo = FALSE, message = FALSE, warning = FALSE}

# alter these plotting defaults as necessary

# bootstrap cutoff; plot boostrap values above this threshold
boot_thresh <- 95

# size of node label text
node_text_size <- 1.75

# nudge node label text horizontally
x_nudge <- 0

# tree scale offset
scale_offset <- 0.1

# tree scale font size
scale_font_size <- 2

# tip label font size
tip_font_size <- 2

```

### COVID-19 Analysis

The analysis of COVID-19 samples has been completed. These results must always be used in conjunction with epidemiological data when determining if isolates are epidemiologically linked. This analysis should not be used as a replacement for a thorough epidemiological investigation.

### SNP Heatmap

The number of Single Nucleotide Polymorphisms (SNPs) between each sample is shown on the heatmap below.

```{r root-tree, echo = FALSE, message = FALSE, warning = FALSE}

# This block midpoint-roots the tree

# read tree and midpoint root
tree <- read.tree(nwk)
mpt <- midpoint.root(tree)

# store midpoint-rooted tree as dataframe
mpt.fort <- fortify(mpt)

# get vertical order of tip labels from tree dataframe
mpt.tip <- mpt.fort[which(mpt.fort$isTip ==  TRUE),]
mpt.ord <- mpt.tip$label[order(mpt.tip$y)]

# store base plot of midpoint-rooted tree
gtree <- ggtree(mpt, branch.length = "none")

```

```{r format-matrix, echo = FALSE, message = FALSE, warning = FALSE}

# replace forward slashes with underscores
row.names(snp_mat) <- gsub("/","_",row.names(snp_mat))
colnames(snp_mat) <- gsub("/","_",colnames(snp_mat))

# order snp matrix by vertical order of tip labels
snp_mat <- snp_mat[c(mpt.ord),c(mpt.ord)]

```

```{r plot-tree-and-heatmap, echo = FALSE, message = FALSE, warning = FALSE}

### Split isolate IDs by delimiter "-" and "_" (for >= 20 isolates)

# ggtree will often crop the figure too small; subtract from ymin and add to ymax to fix this
ymin <- min(gtree$data$y) - 5
ymax <- max(gtree$data$y) + 1

# main tree plotting function
gheatmap(gtree, snp_mat,
    width = heatmap_width,
    offset = tree_offset,
    cell_labels = TRUE,
    cell_font_size = cell_font_size,
    font.size = axis_font_size,
    colnames_angle = 90,
    rownames_angle = 0,
    colnames_offset_y = col_offset,
    rownames_offset_x = row_offset) +

# set heatmap colourbar colors and limits
scale_fill_viridis(limits = c(1,(max(snp_mat)+1)),
    na.value = "white",
    name = "SNPs",
    guide = "colourbar") +

# set plot y limits
ylim(ymin,ymax) +

# remove whitespace around plot and add legend
theme(plot.margin = unit(c(0,0,0,0), "mm"),
    legend.box = "horizontal",
    legend.text = element_text(size = legend_text_size),
    legend.title = element_text(size = legend_title_size),
    legend.position = "bottom",
    legend.margin = margin(0,0,0,0)) +

# place heatmap colourbar beneath the heatmap (rather than beside)
guides(fill = guide_colourbar(title.position = "top",
    title.hjust = 0.5,
    barheight = colourbar_height,
    barwidth = colourbar_width))

ggsave('SNP_heatmap.png', units = "in", width = 8.5, height = 10)

snp_mat <- snp_mat[,ncol(snp_mat):1]
snp_mat <- snp_mat[nrow(snp_mat):1,]
snp_mat$Iso <- rownames(snp_mat)
snp_mat <- snp_mat[,c(ncol(snp_mat),1:(ncol(snp_mat)-1))]
colnames(snp_mat) <- c("",rownames(snp_mat))

write.table(snp_mat,"snp_distance_matrix.tsv",
            row.names = T,
            col.names = T,
            sep = "\t",
            quote = F)
```
\newpage

### Phylogenetic tree

Using variation within the genome between samples (SNPs), we can estimate how related between isolates. We do this by determining if isolates share a similar common ancestor. Here we are looking for isolates that cluster together and share a small amount of horizontal distance on the tree.

```{r plot-tree, echo = FALSE, message = FALSE, warning = FALSE}

# This block plots the midpint-rooted tree with bootstrap values

# main tree plotting function
gtree <- ggtree(mpt, color = "black", alpha = 0.75, size = 0.5) +

# add boostrap values as node labels
#geom_nodelab(aes(x = branch,
#  label = label,
#  subset = !isTip & (as.numeric(label) >= boot_thresh)),
#  vjust = -0.5,
#  nudge_x = x_nudge,
#  size = node_text_size) +

# add tip labels
geom_tiplab(size = tip_font_size) +

# add tree scale
geom_treescale(offset = scale_offset,
    fontsize = scale_font_size,
    y = 0,
    x = 0) +

# remove whitespace around plot
theme(plot.margin = unit(c(0,0,0,0), "cm"))

# ggtree will often crop the figure too small; add to xmax to fix this
# we've found the following function calculates a decent value to add to xmax:

log10_ceiling <- function(x) {
    10^(ceiling(log10(x)))
}

xmax <- max(gtree$data$x) + (log10_ceiling(max(gtree$data$x))/5)
xmin <- 0

# set x limits and plot tree
gtree + xlim(xmin,xmax)
ggsave('ML_tree.png', units = "in", width = 8.5, height = 10)
```

### Methods

The figures shown here were generated using sequence data processed with the [genomic_cluster_analysis pipeline](https://github.com/AndrewLangvt/genomic_analyses/blob/main/workflows/wf_genomic_cluster_analysis.wdl).

The genomic_cluster_analysis pipeline uses [Mafft](https://mafft.cbrc.jp/alignment/software/) to perform multiple-sequence alignment of all SARS-CoV-2 genomes provided. The resulting alignment fasta file is used to generate a pairwise-snp distance matrix with [snp-dists](https://github.com/tseemann/snp-dists) and a maximum-likelihood phylogeneitc tree with [IQ-Tree](http://www.iqtree.org/).

Output from snp-dists and IQ-Tree are curated into a single pdf report using the [Theiagen cluster-report-env](https://hub.docker.com/repository/docker/theiagen/cluster-report-env).