tso500_analysis.Rmd

---
title: "final"
author: "Sophie Paul"
date: "21/02/2022"
output: html_document
---


```{r}
library(tso500R)
library(tidyverse)

cvo_data_dir <- "test_data/cvo_files/211110_A01295_0033_AHLHC5DRXY_TSO500/"
annotation_data_filepath <- "test_data/TSO_Reference.xlsx"
flowcell_barcode <- str_extract(cvo_data_dir, "_\\w{10}_") %>% str_remove_all("_")

annotations <- read_annotation_data(annotation_data_filepath)
cvo_data <- read_cvo_data(cvo_data_dir)

small_variant_df <- read_small_variants(cvo_data) %>%
  process_small_variant_data() %>%
  add_annotation_data(annotations)

plot_af_per_variant_consequence(small_variant_df) %>% add_common_theme_elements()
plot_af_density(small_variant_df) %>% add_common_theme_elements()
plot_af_histogram(small_variant_df) %>% add_common_theme_elements()

metrics_df <- get_metrics_df(cvo_data)
tmb_metric_names <- c("total_tmb", "coding_region_size_in_megabases", "number_of_passing_eligible_variants")
msi_metric_names <- c("usable_msi_sites", "total_msi_sites_unstable", "percent_unstable_msi_sites")

data_to_write <- list(metrics_df %>% select(sample_id, all_of(msi_metric_names)), # MSI data
                      metrics_df %>% select(sample_id, all_of(tmb_metric_names)), # TMB data
                      small_variant_df)

names(data_to_write) <- paste0(flowcell_barcode, c("_MSI", "_TMB", "_Nonsyn"))

write_workbook("test", data_frames = data_to_write, sheet_names = names(data_to_write))
```

```{r}
library(rpivotTable)
rpivotTable(small_variant_df, rows="sample_id", cols=c("consequence_s"), width="100%", height="100%")
```