decay_plot {RNAdecay} | R Documentation |
Plots RNA decay data and/or decay models using the ggplot2 package.
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)
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) |
returns a ggplot to be used with print; could also be modified using the syntax of ggplot2 e.g.'+geom_XXXX(...)'
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)