README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```

# shinyScatterplot
[![Travis-CI Build Status](https://travis-ci.org/lapinskim/shinyScatterplot.svg?branch=master)](https://travis-ci.org/lapinskim/shinyScatterplot)


Recreation of the scatterplot from:


<center>
![Figure 2](inst/img/figure2.png)
</center>


**Figure 2.** published in [*Cytoplasmic polyadenylation-mediated translational control of maternal mRNAs directs maternal to zygotic transition*](http://dev.biologists.org/content/early/2017/12/08/dev.159566) Winata CL, Łapiński M et al., Development, 11 December 2017. 


Interactive plot recreated in Shiny.

### Functions

Two functions are defined as follows. One for calculating the rate of transcription and translation. And second used for plotting.

### Data

The dataset contains the read counts and FPKM values for the conducted experiments. The gene expression was quantified using Salmon[[1](https://combine-lab.github.io/salmon/)], imported to R using tximport[[2](https://github.com/mikelove/tximport)] and normalized with DESeq2[[3](https://bioconductor.org/packages/release/bioc/html/DESeq2.html)]. FPKM values were produced using DESeq2.

## Polysome association dynamics

Measurements of transcription (∆TS) and translation (∆TL) rates were obtained as a fraction of total and polysome-bound expression values at particular stages compared with the egg stage as baseline. Translational regulation is defined as a non-linear relationship  between  transcription and translation rates.

<center>
*transcription rate (∆TS) = total(stage x) / total(egg)*


*translation rate(∆TL) = polysome(stage x) / polysome(egg)*
</center>

## Installation

You can install shinyScatterplot from github with:

```{r gh-installation, eval = FALSE}
# install.packages("devtools")
devtools::install_github("lapinskim/shinyScatterplot")
```

## Example

Run in the interactive session only
```{r examles, eval=FALSE}
if (interactive()) {
    runPlot()
}
```