epiBox: Make Boxplot from Comparison Matrix
In epihet: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

Description Usage Arguments Value Examples

From a user-inputted value, finds the mean of that value for each sample, then creates a boxplot comparing the values for each subtype.

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epiBox(compare.matrix, value, type, box.colors = NULL,
  add.points = FALSE, points.colors = NULL, pdf.height = 10,
  pdf.width = 10, sve = FALSE)

`compare.matrix`	The comparison matrix generated from the compMatrix() function
`value`	The value to be graphed in the boxplot. Possible values are 'read', 'pdr', 'meth', 'epipoly', and 'shannon'
`type`	A dataframe containing the type information for the samples in the comparison matrix. The row names should be the names of the samples and there should be one column containing the type information for each sample.
`box.colors`	A vector of colors to be used as the fill color for each boxplot. If not entered, the default colors of ggplot are used. (default: NULL)
`add.points`	A boolean stating if the individual points for each sample mean should be displayed over the box plots (default: FALSE)
`points.colors`	A vector of colors to be used as the color of the individual points for each sample mean. One color is used per subtype. (default: NULL)
`pdf.height`	An integer representing the height (in inches) of the outputted boxplot pdf file (default: 10)
`pdf.width`	An integer representing the width (in inches) of the outputted boxplot pdf file (default: 10)
`sve`	A boolean to save the plot (default: FALSE)

a data frame containing the mean epigenetic heterogeneity for each sample

comp.Matrix<-data.frame(
p1=c(0.6,0.3,0.5,0.5,0.5,0.6,0.45,0.57,0.45,0.63,0.58,0.67,0.5,0.42,0.67),
p2=c(0.62,0.63,0.55,0.75,0.84,0.58,1,0.33,1,0.97,0.57,0.68,0.73,0.72,0.82),
p3=c(0.72,0.53,0.62,0.69,0.37,0.85,1,0.63,0.87,0.87,0.82,0.81,0.79,
0.62,0.68),
N1=c(0.15,0.24,0.15,0.26,0.34,0.32,0.23,0.14,0.26,0.32,0.12,0.16,0.31,
0.24,0.32),
N2=c(0.32,0.26,0.16,0.36,0.25,0.37,0.12,0.16,0.41,0.47,0.13,0.52,0.42,
0.41,0.23),
N3=c(0.21,0.16,0.32,0.16,0.36,0.27,0.24,0.26,0.11,0.27,0.39,0.5,0.4,
0.31,0.33),
type=rep(c("pdr","epipoly","shannon"),c(5,5,5)),
location=rep(c("chr22-327:350:361:364","chr22-755:761:771:773",
"chr22-761:771:773:781","chr22-821:837:844:849","chr22-838:845:850:858"),
3),stringsAsFactors =FALSE )

subtype <- data.frame(Type= c(rep('CEBPA_sil', 3), rep('Normal', 3)),
row.names <- colnames(comp.Matrix)[1:6],stringsAsFactors = FALSE)

epiBox(compare.matrix = comp.Matrix, value = 'epipoly',
type <- subtype, box.colors = NULL, add.points = FALSE,
points.colors <- NULL, pdf.height = 10, pdf.width = 10,
sve = FALSE)