Description Usage Arguments Details Value Examples
View source: R/stochastic_simulation.R
Automatically plots the result of a simulation for the selected in silico individuals as a heatmap.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
simdf |
The dataframe with the result of the simulation (see |
molecules |
A vector of gene IDs (numeric or character) and/or complex IDs (e.g. CTC1) to be plotted. |
inds |
A vector of in silico individual names for which to plot the expression profiles. |
trials |
A vector of trials ID (= number) to use for the plot (see details). |
timeMin |
Numeric. The minimum simulation time to plot. Default value set to the minimum time in the simulation. |
timeMax |
Numeric. The maximum simulation time to plot. Default value set to the maximum time in the simulation. |
mergeAllele |
Are the gene products originating from different alleles merged? Default TRUE. Also see |
mergePTM |
Are the modified and non-modified versions of the proteins merged? Default TRUE. Also see |
mergeComplexes |
Are the free and in complex gene products merged? Default FALSE. Also see |
yLogScale |
Plot the y-axis in log10-scale? If so, the abundance of each species at each time-point is increased by 1 to avoid zero values. Default TRUE. |
nIndPerRow |
Positive integer, the number of individuals to plot per row. Default 3. |
VirPalOption |
String, palette name option to be passed to |
... |
Any additional parameter to be passed to |
If more than one trial is to be plotted, the mean abundance of each molecule over the different trials is plotted with a solid line, and the min and max abundances represented as coloured areas around the mean.
A plot from ggarrange
.
1 2 3 4 5 6 7 | mysystem = createInSilicoSystem(G = 5, ploidy = 2)
mypop = createInSilicoPopulation(10, mysystem)
sim = simulateInSilicoSystem(mysystem, mypop, 100, ntrials = 5)
plotHeatMap(sim$Simulation,
c(1, 2, 3),
c("Ind1", "Ind2", "Ind3", "Ind4"),
axis.title = element_text(color = "red"))
|
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