decay_plot {RNAdecay} | R Documentation

## decay_plot() function

### 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)

### 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)

### 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)

[Package RNAdecay version 1.3.1 Index]