In lapinskim/shinyScatterplot: Polysome Association Dynamics Plotting

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

shinyScatterplot

Recreation of the scatterplot from:

Figure 2. published in Cytoplasmic polyadenylation-mediated translational control of maternal mRNAs directs maternal to zygotic transition 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], imported to R using tximport[2] and normalized with DESeq2[3]. 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.

transcription rate (∆TS) = total(stage x) / total(egg)

translation rate(∆TL) = polysome(stage x) / polysome(egg)

Installation

You can install shinyScatterplot from github with:

# install.packages("devtools")
devtools::install_github("lapinskim/shinyScatterplot")

Example

Run in the interactive session only

if (interactive()) {
    runPlot()
}

lapinskim/shinyScatterplot documentation built on May 15, 2019, 12:47 p.m.