gauchoReport: View solutions contained within gaucho output

In gaucho: Genetic Algorithms for Understanding Clonal Heterogeneity and Ordering

Description

After running gaucho() on data, this function provides a convenient way to view the solutions and also export them as separate text files and images. For detailed usage, please read the accompanying vignette.

Usage

gauchoReport(gauchoInput, gauchoOutput, outType = "complete",
  yRange = c(-250, 0), output_file_prefix = "")

Arguments

gauchoInput	Raw data analysed by gaucho()
gauchoOutput	Object of class ga produced by gaucho()
outType	Type of output desired - must be one of the following: "complete","fitness","heatmap","phylogeny","proportion"
yRange	Y-axis range when plotting fitness of individuals. Default is c(-250,0)
output_file_prefix	Optional prefix for all output files

Details

This method reports data for the fittest individual; in the event of there being multiple individuals with identical fitness, up to five individuals will be reported. This function's output is governed by the outType argument. All options except for the default "complete" value result in plotting the desired output to the current R session. When outType=="complete", the following output is created for each individual: the full length string, the phylogeny matrix, the proportion matrix, the presence matrix, a heatmap of the raw data with the assigned clones as coloured bars at the side, a stacked barplot showing the proportion of each clone at each timepoint and a plot showing the phylogenetic relationship between the clones. Note that the colours of the clones are consistent across all plots and that the contamination clone (if present) is always the last clone. Also produced is a plot illustrating the change in fitness as the generations evolved.

Value

Nothing is returned.

Author(s)

Alex Murison [e-mail] and Christopher Wardell [e-mail]

See Also

ga-class, ga, gauchoReport, gaucho_simple_data, gaucho_hidden_data, gaucho_synth_data, gaucho_synth_data_jittered, BYB1_G07_pruned

Examples

## The vignette provides far more in-depth explanation and examples ##

## Load the included simple example data
gaucho_simple_data = read.table(file.path(system.file("extdata",package="gaucho"),"gaucho_simple_data.txt"),header=TRUE,row.names=1)

## Run gaucho using 3 clones and a phylogeny with a single root
solution=gaucho(gaucho_simple_data, number_of_clones=3,nroot=1,iterations=1000)

## Create the four output plots
gauchoReport(gaucho_simple_data,solution,outType="fitness")
gauchoReport(gaucho_simple_data,solution,outType="heatmap")
gauchoReport(gaucho_simple_data,solution,outType="phylogeny")
gauchoReport(gaucho_simple_data,solution,outType="proportion")

## Output the solution and plots in the current working directory
# gauchoReport(gaucho_simple_data,solution)

gaucho documentation built on May 2, 2018, 2:37 a.m.