analyse.data-methods: description of function analyse.data

In stela2502/Rscexv: The backend for the SCExV (single cell expression view) server.

description of function analyse.data

Description

This function implements the backend functionallity of the SCExV analyse page.

Usage

analyse.data(
  obj,
  onwhat = "Expression",
  groups.n,
  cmethod,
  clusterby = "MDS",
  ctype = "hierarchical clust",
  beanplots = TRUE,
  move.neg = FALSE,
  plot.neg = TRUE,
  useGrouping = NULL,
  plotsvg = 0,
  mds.type = "PCA",
  geneGroups = NULL,
  ...
)

Arguments

obj	the Rscexv object
onwhat	cluster on weither Expression of FACS data default='Expression'
groups.n	the number of groups to create
cmethod	clustering method
clusterby	which dataset to cluter on (raw or MDS) default='MDS'
ctype	the clzutering type default = 'hierarchical clust'
beanplots	create beanplots or violinplots
move.neg	should the not expressed value be as set to the minimum expression value?
plot.neg	show the not expressing samples in the bean/violinplots?
useGrouping	do not calculate a new grouping - use this column in the samples table (default=NULL)
plotsvg	create svg figures in addition to the png ones (default=0)
mds.type	which mds algorithm to use (PCA, LLE, ISOMAP or ZIFA) default = PCA
geneGroups	the annotation gene group to use in the heatmaps (default = NULL)

stela2502/Rscexv documentation built on July 6, 2022, 9:02 p.m.