Plotting code for results of Epi-GTBN's experiments on simulated datasets

This is the plotting code for my thesis utilizing ggplot2. My working title for that thesis is Epi-GTBN: An Approach of Epistasis Mining Based on Genetic Tabu Algorithm and Bayesian Network

Dependency

ggplot2
reshape2

Input & Tweak

Input

Input should be like 0025HERaccuracy_Example.csv in given files.

By default it will search for 0025HERaccuracy_Example.csv in R default diretory. Maybe getwd() and setwd() could help.

Tweak

Comments in plot.R should act as a good helper. Also, some quick tweaks are presented below.

• Change filename = 0025HERaccuracy_Example to your own dataset's name.
• In colnames(dataset) = c("Method","MAF = 0.1","MAF = 0.2","MAF = 0.3","MAF = 0.4"), Change "Method","MAF = 0.1","MAF = 0.2","MAF = 0.3","MAF = 0.4" to your own dataset's column names.
• In dataset_long = melt(dataset, id.vars = "Method", variable.name = "MAF", value.name = "Accuracy"), change id.vars to your own dataset's first column name; change variable.name to the name for your plots' horizontal axis and value.name to the name for your plots' vertical axis.
• In dataset_long$Method = factor(dataset_long$Method, level = c("AntEpiSeeker", "BEAM", "BOOST", "hill-climbing", "MDR", "SNPRuler", "Epi-GTBN")), change "AntEpiSeeker", "BEAM", "BOOST", "hill-climbing", "MDR", "SNPRuler", "Epi-GTBN" to value of your own dataset's first column.
• In palette = c("#000000", "#E69F00", "#CC99FF", "#D55E00", "#F0E442", "#0072B2", "#009E73"), amount of colors should coincide with amount of values of your own dataset's first column.
• In color = c(palette, palette, palette, palette), palette appears the same as the amount of the rest of your column (other than your first column). Like four times in my case.
• In p = ggplot(dataset_long,aes(x = Method, y = Accuracy))+facet_grid(.~MAF)+, change x = Method, y = Accuracy, .~MAF to your previous configurations (id.vars, value.name and variable.name).

Result Demo