epiMap: Make Pheatmap from Comparison Matrix

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

Description

Creates a pheatmap for the top 'loci.percent' of values of max standard deviation from the comparison matrix generated by compMatrix(). The rows represent the loci of the epiallele and the columns represent the sample names. The columns can be annotated by adding annotation information as a parameter.

Usage

epiMap(compare.matrix, value, annotate = NULL,
  clustering_distance_rows = "euclidean",
  clustering_distance_cols = "euclidean", clustering_method = "complete",
  annotate.colors = NA, color = colorRampPalette(c("blue", "white",
  "red"))(1000), loci.percent = 0.1, show.rows = FALSE,
  show.columns = FALSE, font.size = 6, 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 pheatmap. Possible values are 'read', 'pdr', 'meth', 'epipoly', and 'shannon'.
annotate	A dataframe containing the annotation information for the columns of the pheatmap. The row names must be the names of the samples. The columns (any number) are the annotations. E.g. a column called 'TET2' with factors 'Pos' and 'Neg' for each sample that is positive or negative for the TET2 gene
clustering_distance_rows	Distance measure used in clustering rows.
clustering_distance_cols	Distance measure used in clustering columns.
clustering_method	clustering method used.
annotate.colors	A list containing the colors for the annotation information. Each element in the list is a vector of colors with names that correspond to the columns of 'annotate'.
color	a vector of colors used in heatmap.
loci.percent	The top percentage of loci, as a decimal, to be displayed on the pheatmap based on standard deviation, e.g. a value of 0.20 is equivalent to the top 20% of loci (default: 0.10)
show.rows	A boolean stating if the row names should be displayed on the pheatmap (default: FALSE)
show.columns	A boolean stating if the column names should be displayed on the pheatmap (default: FALSE)
font.size	An integer representing the font size to be used for the pheatmap labels (default: 6)
pdf.height	An integer representing the height (in inches) of the pdf file for the pheatmap (default: 10)
pdf.width	An integer representing the width (in inches) of the pdf file for the pheatmap (default: 10)
sve	A boolean to save the plot (default: FALSE)
...	any arguments in the function pheatmap()

Value

A pheatmap object that contains the tree data for both rows and columns and the final pheatmap plot

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)

pmap = epihet::epiMap(compare.matrix = comp.Matrix,
value = 'epipoly',annotate = subtype,
clustering_distance_rows = "euclidean",
clustering_distance_cols = "euclidean",
clustering_method = "complete",annotate.colors = NA,
color= colorRampPalette(c("blue","white","red"))(1000),
loci.percent = 1, show.rows = FALSE,
show.columns = TRUE, font.size = 15,
pdf.height = 10, pdf.width = 10, sve = TRUE)

xiaowenchenjax/epihet documentation built on May 5, 2019, 9:20 a.m.