barcode.timecourse: Plot abundance of barcode lineages over time.

In jessicaaudreylee/PhenoEvoR: Tools for analysis of NetLogo Pheno-Evo model results

Description

Generates a streamgraph plot displaying the abundance of each unique barcode lineage as a proportion of the population, over time, in a Pheno-Evo experiment. At the initiation of the experiment, each founding cell is given a unique barcode. A barcode lineage consists of a founding cell and all its descendants. Over time, especially with high population turnover, some barcodes go extinct. This plot shows barcodes as different colors, with their proportional abundance as their width along the y-axis, and time on the x-axis.

Usage

barcode.timecourse(NLdata, runnum)

Arguments

NLdata	The full dataframe containing data from all BehaviorSpace experiments at all timepoints, imported from NetLogo.
runnum	The run number of the experiment of interest.

Details

There is not a unique color for each barcode. This plot uses a 12-color palette that is repeated several times to cover all the barcodes. However, each lineage "stream" is bordered by a black line, so if two lineages that happen to have the same color end up adjacent, they can be distinguished by the border between them.

Value

A ggplot object using [ggTimeSeries::stat_steamgraph()].

Examples

data(PhenoEvoData_4)
barcode.timecourse(PhenoEvoData_run4, 4)

jessicaaudreylee/PhenoEvoR documentation built on Sept. 7, 2020, 3:50 a.m.