bnpathplot: bnpathplot

In noriakis/CBNplot: plot bayesian network inferred from gene expression data based on enrichment analysis results

bnpathplot

Description

Plot pathway relationship

Usage

bnpathplot(
  results,
  exp,
  expSample = NULL,
  algo = "hc",
  algorithm.args = NULL,
  expRow = "ENSEMBL",
  cl = NULL,
  returnNet = FALSE,
  otherVar = NULL,
  otherVarName = NULL,
  qvalueCutOff = NULL,
  adjpCutOff = 0.05,
  nCategory = 15,
  R = 20,
  interactive = FALSE,
  color = "p.adjust",
  cexCategory = 1,
  cexLine = 0.5,
  chooseDir = FALSE,
  showDir = FALSE,
  delZeroDegree = TRUE,
  labelSize = 4,
  layout = "nicely",
  onlyDf = FALSE,
  disc = FALSE,
  tr = NULL,
  remainCont = NULL,
  shadowText = TRUE,
  bgColor = "white",
  textColor = "black",
  compareRef = FALSE,
  strThresh = NULL,
  strType = "normal",
  hub = NULL,
  scoreType = "bic-g",
  databasePal = "Set2",
  dep = NULL,
  sizeDep = FALSE,
  orgDb = org.Hs.eg.db,
  bypassConverting = FALSE,
  useSiGN = FALSE,
  edgeLink = TRUE,
  cellLineName = "5637_URINARY_TRACT",
  strengthPlot = FALSE,
  nStrength = 10,
  seed = 1
)

Arguments

results	the enrichment analysis result
exp	gene expression matrix
expSample	candidate rows to be included in the inference default to all
algo	structure learning method used in boot.strength() default to "hc"
algorithm.args	parameters to pass to bnlearn structure learnng function
expRow	the type of the identifier of rows of expression matrix
cl	cluster object from parallel::makeCluster()
returnNet	whether to return the network
otherVar	other variables to be included in the inference
otherVarName	the names of other variables
qvalueCutOff	the cutoff value for qvalue
adjpCutOff	the cutoff value for adjusted pvalues
nCategory	the number of pathways to be included
R	the number of bootstrap
interactive	whether to use bnviewer (default to FALSE)
color	color of node, default to adjusted p-value
cexCategory	scaling factor of size of nodes
cexLine	scaling factor of width of edges
chooseDir	if undirected edges are present, choose direction of edges
showDir	show the confidence of direction of edges
delZeroDegree	delete zero degree nodes
labelSize	the size of label of the nodes
layout	ggraph layout, default to "nicely"
onlyDf	return only data.frame used for inference
disc	discretize the expressoin data
tr	Specify data.frame if one needs to discretize as the same parameters as the other dataset
remainCont	Specify characters when perform discretization, if some columns are to be remain continuous
shadowText	whether to use shadow text for the better readability (default: TRUE)
bgColor	color for text background when shadowText is TRUE
textColor	color for text when shadowText is TRUE
compareRef	whether compare to the reference network between pathway
strThresh	threshold for strength, automatically determined if NULL
strType	"normal" or "ms" for multiscale implementation
hub	change the shape of node according to hub scores (default NULL)
scoreType	score type to use on choosing edge direction
databasePal	palette to be used in scale_color_brewer when the multiple results are to be shown
dep	the tibble storing dependency score from library depmap
sizeDep	whether to reflect DepMap score to the node size
orgDb	perform clusterProfiler::setReadable based on this organism database
bypassConverting	bypass the symbol converting If you use custom annotation databases that does not have SYMBOL listed in keys. ID of rownames and those listed in EA result must be same.
useSiGN	default to FALSE. For using SiGN-BN in the function in Windows 10/11, 1. Download the SiGN-BN HC+BS binary in WSL (https://sign.hgc.jp/signbn/download.html) 2. Set PATH to executable (sign.1.8.3)
edgeLink	whether to set edge to geom_edge_link() FALSE to use geom_edge_diagonal()
cellLineName	the cell line name to be included
strengthPlot	append the barplot depicting edges with high strength
nStrength	specify how many edges are included in the strength plot
seed	A random seed to make the analysis reproducible, default is 1.

Value

ggplot2 object

Examples

data("exampleEaRes");data("exampleGeneExp")
res <- bnpathplot(results = exampleEaRes, exp = exampleGeneExp,
                  R = 10, expRow = "ENSEMBL")

noriakis/CBNplot documentation built on Oct. 10, 2024, 12:21 p.m.