Make3D4obj-methods: description of function Make3D4obj

In stela2502/BioData: The package allows to annotate a numeric data.table with col and row data

Description

This function created a MDS 3D plot with an inbuilt background describing the data colors

Arguments

x	the BioData object
group	the grouping value (either colname from the samples table or a rowname from the data table
mds.type	the mds type to use (names from names(x$usedObj$MDS)) default = PCA
cex	define the size of the strings default=0.5
colFunc	the color function if the color is not already defined using colors_4() default= function(x)rainbow(x)
cut	this has to be true for genes, as the samples are then binned into 10 expression groups each containing the same number of samples default=F
names	if true not dots, but the name in the samples table is plotted in 3D default=F
opath	create a webgl representation of the plot in a html page in this path (default = NULL)
main	the title of the plot (default =”)
genes	use gene level MDS data not sample level (default = FALSE)
plotType	choose one [1,2] and check whether you like it ;-) default=1
size	the size of the 3D points default = 3.0
green	single cell normalization looses gene expression values. Display the cells with lost expression in green or black default=FALSE
useRaw	base the projection on the raw data and not the n=100 PCA data (default FALSE)

stela2502/BioData documentation built on Feb. 23, 2022, 5:47 a.m.