plotTsne: Plot TSNE

In AllenInstitute/mfishtools: Building Gene Sets and Mapping mFISH Data

Plot TSNE

Description

Plot a TSNE of the data, with assigned colors and labels from provided variables. Note that this function is a modification of code from Pabloc (https://www.r-bloggers.com/author/pabloc/) from https://www.r-bloggers.com/playing-with-dimensions-from-clustering-pca-t-sne-to-carl-sagan/

Usage

plotTsne(
  datIn,
  colorGroup = "none",
  labelGroup = "none",
  useScaled = FALSE,
  capValue = Inf,
  perplexity = 10,
  theta = 0.5,
  main = "TSNE plot",
  maxNchar = 1000,
  seed = 10
)

Arguments

datIn	a fishScaleAndMap output list
colorGroup	a character vector (or factor) indicating how to color the Tsne (e.g., cluster call) or a metadata/mappingResults column name (default=NULL)
labelGroup	a character vector (or factor) indicating how to label the Tsne (e.g., cluster call) or a metadata/mappingResults column name (default=NULL)
useScaled	plot the scaled (TRUE) or unscaled (FALSE; default) values
capValue	values above capValue will be capped at capValue (default is none)
perplexity, theta	other parameters for Rtsne
main	title of the plot
maxNchar	what is the maximum number of characters to display in the plot for each entry?
seed	for reproducibility

Value

Only returns if there is an error

AllenInstitute/mfishtools documentation built on July 5, 2023, 4:20 p.m.