tsne {M3C} | R Documentation |
tsne: A tsne function
tsne(mydata, K = FALSE, labels = FALSE, perplex = 15, printres = FALSE, seed = FALSE, axistextsize = 30, legendtextsize = 30, dotsize = 6, textlabelsize = 4)
mydata |
Data frame or matrix or M3C results (list) object: if dataframe/matrix should have samples as columns and rows as features |
K |
Numerical value: if running on the M3C results object, which value was the optimal K? Needs manual input from user. |
labels |
Factor: if we want to just display gender for example, only for when running without K parameter and with a matrix or data frame |
perplex |
Numerical value: this is the perplexity parameter for tsne, it usually requires adjusting for each dataset |
printres |
Logical flag: whether to print the plot into current directory |
seed |
Numerical value: to repeat the results exactly, setting seed is required |
axistextsize |
Numerical value: axis text size |
legendtextsize |
Numerical value: legend text size |
dotsize |
Numerical value: dot size |
textlabelsize |
Numerical value: text inside plot label size |
A tsne plot object
TSNE <- tsne(mydata,perplex=15)