pseudotimeTest3D-methods: description of function pseudotimeTest3D

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

Description

Calculate and plot pseudotime relevant information.

Arguments

x	a BioData object (preferably a SingleCells object)
a	the first time defining vector (e.g. a MDS dimension)
b	the second time defining vector (e.g. a MDS dimension)
grouping	a samples grouping to color the Pseudotime plot.
outpath	a outpath for the files default=x$outpath
n	how many genes to plot on both sides default=100
plotGenes	additional default genes to plot default=NULL
smooth	roling smoothing window size (default 100)
invert	invert the time before usage ( default=FALSE)
cleanFolder	remove all files from the outpout folder before creating new ones (default FALSE)
plotType	( 'png', 'png_high_res', 'pdf' )
summaryPlot	the name of the summary plot file ( default NULL no summary plot)

Details

A simple pseudotime analysis based on a linear model, that can create the pseudotime from the two varibales 'a' and 'b'

fit = loess( b~a )

The fitted values will be used as pseudotime and the pseudotiume is plotted versus the two defininge variables to the file outpath/Pseudotime.png using the grouping color. Pseudotime is depicted as bluered line indicating the orientation blue -> red.

The pseudotime will be added into the samples table and the correlation to the pseudotime will be added to the annotation table (both replacing old data!).

The function returns the top/bottom (n) correlating genes.

The rolling mean values that are summing up only expression values from one group are colored in the group colour all others are black.

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