---
title: "demo"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{demo}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

```{r setup}
library(knitr)
library(mhcnuggetsr)
library(testthat)
```

For this vignette, we use the same example as the MHCnuggets
Python notebooks.

Get the path to the testing peptides, and show them:

```{r}
if (is_mhcnuggets_installed()) {
  peptides_path <- get_example_filename("test_peptides.peps")
  expect_true(file.exists(peptides_path))
  readLines(peptides_path, warn = FALSE)
}
```

Pick an MHC-I haplotype:

```{r pick_mhc_1_haplotype}
if (is_mhcnuggets_installed()) {
  mhc_1_haplotype <- "HLA-A02:01"
  expect_true(mhc_1_haplotype %in% get_trained_mhc_1_haplotypes())
}
```

Predict:

```
#{r mhc1_predict_ic50_from_file_no_ba_models}
if (is_mhcnuggets_installed()) {
  mhcnuggets_options <- create_mhcnuggets_options(
    mhc = mhc_1_haplotype
  )
  df <- predict_ic50_from_file(
    peptides_path = peptides_path,
    mhcnuggets_options = mhcnuggets_options
  )
  kable(df)
}
```

Predict:


```
#{r mhc1_predict_ic50_from_file_ba_models}
if (is_mhcnuggets_installed()) {
  mhcnuggets_options <- create_mhcnuggets_options(
    mhc = mhc_1_haplotype,
    ba_models = TRUE
  )
  df <- predict_ic50_from_file(
    peptides_path = peptides_path,
    mhcnuggets_options = mhcnuggets_options
  )
  kable(df)
}
```

Use MCH-II haplotype:

```{r pick_mhc_2_haplotype}
if (is_mhcnuggets_installed()) {
  mhc_2_haplotype <- "HLA-DRB101:01"
  expect_true(mhc_2_haplotype %in% get_trained_mhc_2_haplotypes())
}
```

Predict:


```
#{r mhc2_predict_ic50_from_file_no_ba_models}
if (is_mhcnuggets_installed()) {
  mhcnuggets_options <- create_mhcnuggets_options(
    mhc = mhc_2_haplotype
  )
  df <- predict_ic50_from_file(
    peptides_path = peptides_path,
    mhcnuggets_options = mhcnuggets_options
  )
  kable(df)
}
```

Use another MHC-I haplotype. In this case, MHCnuggets has not been
trained upon it, but it is a valid supertype:

```{r pick_mhc_1_haplotype_supertype}
if (is_mhcnuggets_installed()) {
  mhc_1_haplotype <- "HLA-A02:60"
  expect_false(mhc_1_haplotype %in% get_trained_mhc_1_haplotypes())
}
```

Predict:

```
#{r predict_mhc_1_haplotype_supertype}
if (is_mhcnuggets_installed()) {
  mhcnuggets_options <- create_mhcnuggets_options(
    mhc_class = "I",
    mhc = mhc_1_haplotype
  )
  df <- predict_ic50_from_file(
    peptides_path = peptides_path,
    mhcnuggets_options = mhcnuggets_options
  )
  kable(df)
}
```

## Appendix

### All example files

```{r}
if (is_mhcnuggets_installed()) {
  basename(get_example_filenames())
}
```

### All MHC-I haplotypes

These are the MHC-I haplotypes that have a trained model.

```{r}
if (is_mhcnuggets_installed()) {
  cat(get_trained_mhc_1_haplotypes())
}
```

### All MHC-II haplotypes

These are the MHC-II haplotypes that have a trained model.

```{r}
if (is_mhcnuggets_installed()) {
  cat(get_trained_mhc_2_haplotypes())
}
```

### Session info

```{r}
mhcnuggetsr_report()
```
