---
title: "Generate signatures"
author: "Tiago Maié"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Generate signatures}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---



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

## CimpleG (Simple CpG signatures)

* CimpleG tries to find the CpGs that best classify a cell-type given a train dataset
* It also enables you to perform cell-type deconvolution in a couple of easy steps
* It can use beta or M values
* Here we show how easy it is to generate a signatures

### Installation

If you haven't installed CimpleG, you can find the instructions to do so [here](https://costalab.github.io/CimpleG/#installation).
However it should be as simple as:

```{r install_cimpleg, eval=FALSE}
if (!require("CimpleG")) devtools::install_github("costalab/CimpleG")
```

### Loading package

We load the CimpleG package.

```{r load_cimpleg}
library("CimpleG")
```

### Loading data

In this tutorial, we will use a small dataset with just 409 samples and 1000 CpGs.
We will also use a table with metadata regarding these samples.
This dataset comes included with CimpleG. You can read more about it here: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15396278.svg)](https://doi.org/10.5281/zenodo.15396278).


```{r load_data}
# load data
data(train_data)
data(train_targets)
```

### Running CimpleG

Running CimpleG can be quite simple. You just need to run the CimpleG function with a few parameters.

```{r cimpleg}
# run CimpleG
cimpleg_result <- CimpleG(
  train_data,
  train_targets,
  target_columns = c("blood_cells", "hepatocytes"),
  train_only = TRUE
)
```

Here we are generating signatures to find leukocytes and hepatocytes.

### Plotting CimpleG CpG signature
We can quickly visualize how our signature is able to separate the data.

```{r plot_cimpleg, fig.width=4, fig.height=6}
sig_plt <-
  signature_plot(
    cimpleg_result,
    train_data,
    train_targets,
    sample_id_column = "gsm",
    true_label_column = "cell_type"
  )
sig_plt$plot
```