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.
Two functions are defined as follows. One for calculating the rate of transcription and translation. And second used for plotting.
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.
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)
You can install shinyScatterplot from github with:
# install.packages("devtools")
devtools::install_github("lapinskim/shinyScatterplot")Run in the interactive session only
if (interactive()) {
runPlot()
}