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RMarkdown file showing the nirs data analysis
---
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()
```
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