t-Distributed Stochastic Neighbor embedding with tSNEplot

This function computes and plots t-Distributed Stochastic Neighbor embedding (t-SNE) analysis for unsupervised nonlinear dimensionality reduction of count expression matrix. Internally, it is applied the Rtsne::Rtsne() function, using the exact t-SNE computing with theta=0.0.

tSNEplot(
  countMatrix,
  targets,
  plotly = FALSE,
  savePlot = FALSE,
  filePlot = NULL,
  ...
)

Arguments

countMatrix	`date.frame` or `matrix` containing raw read counts.
targets	targets `data.frame`.
plotly	logical: when `FALSE` (default), the `ggplot2` plot will be returned. `TRUE` option returns the `plotly` version of the plot.
savePlot	logical: when `FALSE` (default), the plot will not be saved. If `TRUE` the plot will be saved, and requires the `filePlot` argument.
filePlot	file name where the plot will be saved. For more information, please consult the `ggplot2::ggsave()` function.
...	additional parameters for the `Rtsne::Rtsne()` function.

Value

returns an object of ggplot or plotly class.

References

Jesse H. Krijthe (2015). Rtsne: T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation, URL: https://github.com/jkrijthe/Rtsne

Examples

targetspath <- system.file("extdata", "targets.txt",
package = "systemPipeR")
targets <- read.delim(targetspath, comment = "#")
cmp <- systemPipeR::readComp(file = targetspath, format = "matrix",
delim = "-")
countMatrixPath <- system.file("extdata", "countDFeByg.xls",
package = "systemPipeR")
countMatrix <- read.delim(countMatrixPath, row.names = 1)
set.seed(42)
tSNEplot(countMatrix, targets, perplexity = 5)