nice_tSNE: Function to make tSNE plots.

In davidrequena/drfun: Functions To Help With RNAseq Data Analysis

Function to make tSNE plots.

Description

Function to make tSNE plots.

Usage

nice_tSNE(
  object,
  seed = 0,
  perplexity = 3,
  max_iterations = 10000,
  returnData = FALSE,
  variables = c(fill = "VarFill", shape = "VarShape"),
  colors = NULL,
  shapes = NULL,
  size = 7,
  alpha = 1,
  legend_names = c(fill = "Label Fill", shape = "Label Shape"),
  legend_title = 20,
  legend_elements = 16,
  legend_pos = c(0.8, 0.8, "right"),
  labels = NULL,
  name_tags = NULL
)

Arguments

object	A DEseq object already transformed with the variance stabilizing or rlog transformations.
seed	To set the random seed.
perplexity	The average number of samples by patient (neighbors in a set).
max_iterations	Maximum number of iterations to perform.
returnData	Indicates if the function should return the data (TRUE) or the plot (FALSE). Default: FALSE.
variables	To indicate the variables to be used as Shape and Fill of the markers.
colors	Vector of colors to be used for the categories of the variable assigned as Marker Fill.
shapes	Vector of shapes to be used for the categories of the variable assigned as Marker Shape.
size	Size of the marker. Default: 7.
alpha	Transparency of the marker, which goes from 0 (transparent) to 1 (no transparent). Default: 1.
legend_names	The names to be used for the legend of the Shape and Fill.
legend_title	Font of the legend title. Default: 20.
legend_elements	Font of the elements of the legend Default: 16.
legend_pos	Position of the legend in the plot. Default: c(0.80, 0.80, "right").
labels	A vector containing the variable to be used as labels (name inside the marker), and the label size. Example: c(var = "patient", size = 2). Default: NULL (no labels).
name_tags	A vector containing the variable to be used as name tags (name outside the marker), tag size, minimum distance in order to add an arrow connecting the tag and the marker, and minimum distance from the tag and the center of the marker. Example: c(var = "label", size = 3, minlen = 2, box = 0.5). Default: NULL (no name tags).

davidrequena/drfun documentation built on May 15, 2024, 10:33 a.m.