alluvialMat: alluvialMat

In genesofeve/projectR: Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering

alluvialMat

Description

Function to provide alluvial matrix for generating alluvial plot

Usage

alluvialMat(
  projection,
  annotations,
  annotationName = "Cell type",
  annotationType = "Cell",
  plot = TRUE,
  minPropExplained = 0.75,
  pvalThreshold = 0.05,
  qvalThreshold = 0.05
)

Arguments

projection	a projection generated from projectR, ensure that full = TRUE while generating projection
annotations	a character vector of annotations for the data
annotationName	a charcter fof collective name of the annotations, default is "Cell type"
annotationType	a character indicating the type of data annotated, default is "Cell"
plot	logical indicating whether to return the alluvial plot, default is TRUE
minPropExplained	threshold for minimum proportion of samples that correspond to a pattern to be used for plotting
pvalThreshold	theshold level of significance for p-value
qvalThreshold	theshold level of significance for Benjamini-Hochberg corrected p-value

Value

A matrix to generate alluvial plots

Examples

projection <- projectR(data=p.ESepiGen4c1l$mRNA.Seq,loadings=AP.RNAseq6l3c3t$Amean,
dataNames = map.ESepiGen4c1l[["GeneSymbols"]], full = TRUE)
alluvialMat(projection,pd.ESepiGen4c1l$Condition)

genesofeve/projectR documentation built on Nov. 16, 2024, 8:20 p.m.