qcSmallClusters: Computing of the fraction of clusters with low number of...

In tchitchek-lab/SPADEVizR: SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results

Computing of the fraction of clusters with low number of associated cells

Description

Computes the fraction of clusters having a number of associated cells less than a specific threshold (th.size parameter).

Usage

qcSmallClusters(Results, clusters = NULL, th.size = 50,
  PDFfile = "qcSmallClusters.pdf",
  width = ncol([e-mail]),
  height = nrow([e-mail])/4, tile.color = "black")

Arguments

Results	a Results object
clusters	a character vector containing the clusters names to be computed (by default all clusters will be computed)
th.size	a numeric value specifying the minimum number of cells needed for a cluster to be considered a a small cluster
PDFfile	a character specifying the location of the output PDF path
width	a numeric specifying the plot width in the output PDF file
height	a numeric specifying the plot height in the output PDF file
tile.color	a character specifying the border color of the tiles (NA to remove tile borders)

Details

This function can also generate a PDF file summarizing the results.

Value

a list containing a numeric (perc numeric element) containing the fraction of clusters having a number of associated cells less than the threshold and a dataframe (small.clusters element) specifying the clusters having a number of associated cells less than the threshold

tchitchek-lab/SPADEVizR documentation built on Jan. 27, 2024, 8:58 p.m.