epiBox: Make Boxplot from Comparison Matrix

In TheJacksonLaboratory/epihet: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

Description

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

Usage

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

Arguments

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)

Value

a data frame containing the mean epigenetic heterogeneity for each sample

Examples

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)

TheJacksonLaboratory/epihet documentation built on Dec. 22, 2020, 1:10 p.m.