RMarkdown file showing the nirs data analysis

loading_and_plotting_nirs_data.Rmd

---
title: "Loading and plotting nirs data"
author: "Eryk Walczak"
date: "18 December 2016"
output:
  html_document: default
  pdf_document: default
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, message = FALSE, warning = FALSE)
```

## Loading

Install the necessary packages if not available:

```{r}
# install.packages("R.matlab")
library(R.matlab)
```

Load the nirs file
```{r}
data <- readMat("Simple_Probe.nirs")
```

Nirs format description is available [here](http://www.nmr.mgh.harvard.edu/martinos/software/homer/HOMER2_UsersGuide_121129.pdf#4)

## Exploring

Get the available variable names
```{r}
names(data)
```

Find the dimensions of data: samples and channels

```{r}
dim(data$d)

# number of channels
ncol(data$d)
```

## Plotting

Create a custom plotting function

```{r}
myPlot <- function(y){
  plot(data$t, y,
       type = "l",
       xlab = "Time", ylab = "Intensity",
       ylim = c(range(data$d)),
       main = paste("Channel ", toString(y)))
  # add the lines when triggers occur
  lines(data$t, data$s*1500, # multiply the trigger value to make it visible
        type = "l", xlab = "Time", col = "red")
}
```

Apply the plotting function to all channels

```{r}
apply(data$d[, 1:ncol(data$d)], 2, myPlot)
```

Session info:

```{r}
sessionInfo()
```