epiTSNE: Make TSNE Plot from Comparison Matrix

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

Description

From a user-inputted value, creates a TSNE plot from the sample data and colors each point by the subtype information provided.

Usage

epiTSNE(compare.matrix, value, type, points.colors = NULL, theta = 0.5,
  curTheme = NULL, perplexity = 5, max_iter = 1000,
  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 PCA plot
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.
points.colors	A vector of colors to be used as the color of the individual points for each sample. One color is used per subtype. (default: NULL)
theta	A decimal representing the theta parameter for the Rtsne() function. Represents the speed/accuracy trade-off (0.0 is exact TSNE) (default: 0.5)
curTheme	the theme of ggplot2 to control control the appearance of all non-data components of the plot
perplexity	An integer representing the perplexity parameter for the Rtsne() function (default: 30)
max_iter	An integer representing the max_iter parameter for the Rtsne() function. Represents the number of iterations (default: 1000)
pdf.height	An integer representing the height (in inches) of the outputted TSNE plot pdf file (default: 10)
pdf.width	An integer representing the width (in inches) of the outputted TSNE plot pdf file (default: 10)
sve	A boolean to save the plot (default: FALSE)

Value

A T-SNE 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)

epiTSNE(compare.matrix = comp.Matrix, value = 'epipoly',
type = subtype, points.colors = NULL, theta = 0.5,
perplexity = 1, max_iter = 1000, pdf.height = 10,
pdf.width = 10, sve = TRUE)

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