---
title: Reproduce the Diffusion Map vignette with the supplied data()
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Reproduce the Diffusion Map vignette with the supplied data()}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(fig.width=6, fig.asp=0.7)
```

Quickstart
==========

A short version to achive the above is by using the preprocessed version of the dataset provided with this package. `data(guo)` is already preprocessed (using the method first mentioned), has its threshold set to a constant 15 and is ready to use. Since the platform’s maximum amplification cycles are 40, that number can be used as upper border of the uncertainty range.

```{r}
library(destiny)
data(guo)
```

It can be used directly for diffusion map creation:

```{r}
dm_guo <- DiffusionMap(guo, verbose = FALSE,
                       censor_val = 15, censor_range = c(15, 40))
dm_guo
```

```{r}
plot(dm_guo)
```

using the annotation shows that the approximation worked

```{r}
palette(cube_helix(6))
plot(dm_guo, col_by = 'num_cells',
     legend_main = 'Cell stage')
```

References
==========

