decay_plot: decay_plot() function

In RNAdecay: Maximum Likelihood Decay Modeling of RNA Degradation Data

Description

Plots RNA decay data and/or decay models using the ggplot2 package.

Usage

decay_plot(
  geneID,
  xlim = c(0, 500),
  ylim = c(0, 1.25),
  xticks = NA,
  yticks = 0:5/4,
  alphaSZ = 8,
  what = c("Desc", "models", "reps", "meanSE", "alphas&betas"),
  DATA,
  treatments = NA,
  colors = NA,
  mod.results = NA,
  gdesc = NA,
  desc.width = 55
)

Arguments

geneID	single gene ID from data set (e.g. "AT1G00100") for which to plot data/model
xlim, ylim	vector of length 2 defineing the limits of the plot (zooms in on data)
xticks, yticks	vectors specifyng tick marks for the x and y axes
alphaSZ	text size of alpha and beta parameter labels if plotted
what	character vector specifying what to plot; any or all (default) of "Desc","models","reps","meanSE","alphas&betas" "Desc" - plots gene descriptions behind data "models" - plots the selected fit model "reps" - plots individual replicate data as distinct shapes "meanSE - plots the replicate means and standard errors "alphas&betas" - plots the values of the alphas and betas for each model below the model at the greatest x position
DATA	(required) normalized abundance decay data with column names: "geneID", "treatment","t.decay", "rep","value"
treatments	what treatments/genotypes to plot from the supplied data
colors	vector of R recognized colors (e.g. "red","darkblue")
mod.results	(optional; required for plotting models) data.frame of the model results as output from the modeling (e.g. "alphas+betas+mods+grps+patterns+relABs.txt")
gdesc	(optional; required for plotting gene descriptions) gene descriptions (geneID-named vector of gene descriptions geneID must match those of data)
desc.width	width of gene descriptions (in number of characters) before word wrap

Value

returns a ggplot to be used with print; could also be modified using the syntax of ggplot2 e.g.'+geom_XXXX(...)'

Examples

p<-decay_plot("Gene_BooFu",
          mod.results = data.frame(alpha_WT = 0.0830195, beta_WT = 0.04998945,
                                   model = 1, alpha_grp = 1, beta_grp = 1, alpha_subgroup = 1.1,
                                   row.names = "Gene_BooFu"),
          what = c("meanSE","alphas&betas","models"),
          treatments = "WT",
          colors = "black",
          DATA = data.frame(geneID=rep("Gene_BooFu",15),
                            treatment=rep("WT",15),
                            t.decay=rep(c(0,7.5,15,30,60),3),
                            rep=paste0("rep",c(rep(1,5),rep(2,5),rep(3,5))),
                            value= c(0.9173587, 0.4798672, 0.3327807, 0.1990708, 0.1656554,
                                     0.9407511, 0.7062988, 0.3450886, 0.3176824, 0.2749946,
                                     1.1026497, 0.6156978, 0.4563346, 0.2865779, 0.1680075)),
          xlim = c(0, 65),
          alphaSZ = 10)
print(p)

RNAdecay documentation built on Nov. 8, 2020, 5:52 p.m.