paracrine-autocrine-functions: get Cell Expression Signature

In cavei/cellCB: Cell City Band

get Cell Expression Signature

Description

get Cell Expression Signature

Define gene behaviour in the cell

Define ligand receptor behaviour in the cell

Assign color to the nodes

Assign color to the nodes

Assign color to the nodes

Assign color to the nodes

Merge time points wisely

Merge time points wisely

Merge time points wisely

Render Html Video

Render the video

Usage

getCellExpressionSignature(
  RData = "rpkm-Rdatas/all-wt.RData",
  objname = "all_wt",
  cols = 1:4
)

extractGenesBehavious(activeAtDays, activeAtDaysTot, constitutiveWide)

extractLigandReceptorBehaviours(genesBehaviours, db)

assignColorCode(ligandReceptorBehaviours, paletteName = "Greens")

assignCellCode(ligandReceptorBehaviours, cell)

resolveWarnings(lrCols, ligands, receptors)

removeElement(namedVector, nms)

wiseMergeTimePoints(ligandReceptorBehaviours)

paraWiseMergeTimePoints(
  ligandReceptorBehavioursCell,
  ligCell = "fap",
  recCell = "ec"
)

paraWiseMultiMergeTimePoints(
  ligandReceptorBehavioursCell,
  ligCells = c("ec", "fap", "mp", "inf", "per"),
  recCell = "ec",
  removeAutocrine = TRUE,
  useConstitutiveLigands = FALSE
)

renderHTMLvideo(
  ligandsReceptorCumulative,
  receptorGraph,
  lrCols,
  lrCell = NULL,
  cell,
  condition
)

renderHTMLvideo2.0(ligandsReceptorCumulative, receptorGraph, cell, condition)

Arguments

RData	an data RData
objname	the loaded object name
cols	columns to use
activeAtDays	list of gene active at days
activeAtDaysTot	list of gene active in total tissue
constitutiveWide	constitutive active genes
genesBehaviours	list of gene active at days from extractGenesBehavious
db	the ligand receptor database
ligandReceptorBehaviours	list of ligand and receptor ativation
paletteName	the name of the palette to use.
cell	cell name
lrCols	dictionary of ligand receptor colors
ligands	vector of ligands
receptors	vector of receptors
namedVector	named vector
nms	names
ligandReceptorBehavioursCell	list of ligand enad receptor ativation
ligCell	cell that produce the ligands
recCell	cell that produce the receptors
ligCells	cells that produce the ligands
removeAutocrine	if TRUE remove aoutocrine loops
useConstitutiveLigands	if TRUE use constitutive ligands
ligandsReceptorCumulative	list of ligand receptors per day
receptorGraph	the graph receptor
lrCell	dictionary of ligand receptor cells
condition	cell condition

cavei/cellCB documentation built on Sept. 14, 2023, 8:15 a.m.