epiTSNE: Make TSNE Plot from Comparison Matrix
In epihet: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

Description Usage Arguments Value Examples

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

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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)

`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)

A T-SNE plot

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)