11-scCUTseq_brca-phylo.Rmd

# Phylogenetic analysis of breast cancer

This sections produces all the figures used in Supplementary Figure 10.

```{r}
# Source setup file
source("./functions/setup.R")

# Load functions
source("./functions/plotHeatmap.R")
```

## Performing phylogenetic analysis

We performed phylogenetic analysis of the single-cells of two breast cancer samples using MEDICC2. The input for this the total copy number profiles and the following command was used to run this.

```{bash performing phylo analysis, eval = FALSE}
medicc2 --plot none -j {nthreads} --total-copy-numbers -a 'total_cn' {input_tsv} {output_dir}
```

## Plotting phylogenetic tree and heatmap

We then plot the tree generated by MEDICC2 alongside the single-cell genomewide heatmap. First we plot sample 1.

```{r plot trees and heatmap brca1, fig.width=22, fig.height=14}
# Load in brca1 data
tree = read.tree("./data/phylotrees/brca1_500kb.new")
input = fread("./data/phylotrees/brca1_input.tsv")

# Reorder
dt = dcast(input, chrom + start + end ~ sample_id)
dt = dt[gtools::mixedorder(chrom),]

# Rename column and set chr23 back to chrX
setnames(dt, "chrom", "chr")
dt[chr == "chr23", chr := "chrX"]

# include diploid
dt[, diploid := 2L]
dt[chr == "chrX", diploid := 1L]

# Plot tree
tree_plot = ggtree(tree)

# Get sample order from tree
col_order = rev(get_taxa_name(tree_plot))

# Plot heatmap
heatmap = plotHeatmap(dt[, 4:ncol(dt)], dt[, 1:3], dendrogram = F, order = col_order, linesize = .75)

# Combine plots
tree_plot + heatmap + plot_layout(widths = c(1, 3))
```

Next, we do the same but for sample 2.

```{r plot trees and heatmap brca2, fig.width=22, fig.height=8}
# Load in brca1 data
tree = read.tree("./data/phylotrees/brca2_500kb.new")
input = fread("./data/phylotrees/brca2_input.tsv")

# Reorder
dt = dcast(input, chrom + start + end ~ sample_id)
dt = dt[gtools::mixedorder(chrom),]

# Rename column and set chr23 back to chrX
setnames(dt, "chrom", "chr")
dt[chr == "chr23", chr := "chrX"]

# include diploid
dt[, diploid := 2L]
dt[chr == "chrX", diploid := 1L]

# Plot tree
tree_plot = ggtree(tree)

# Get sample order from tree
col_order = rev(get_taxa_name(tree_plot))

# Plot heatmap
heatmap = plotHeatmap(dt[, 4:ncol(dt)], dt[, 1:3], dendrogram = F, order = col_order, linesize = .75)

# Combine plots
tree_plot + heatmap + plot_layout(widths = c(1, 3))
```