GetResultTgCrosstalk: Filter Important Gene Pairs in One Interaction

In ZJUDBlab/InterCellDB: Tool and Database for Analyzing Interactions

Filter Important Gene Pairs in One Interaction

Description

This function help filter and rank the important gene pairs by evaluating both power and confidence, which is calculated from 'LogFC' and 'PVal' respectively.

Usage

GetResultTgCrosstalk(
  object,
  direction.X.to.Y = NULL,
  bound.to.use = list(Power = c(-Inf, Inf), Confidence = c(-Inf, Inf)),
  func.to.use = list(Power = function(x) {     x }, Confidence = function(x) {     1/(1
    + x) }),
  plot.X.to.Y = TRUE,
  axis.order.xy = c("AlphaBet", "AlphaBet"),
  axis.order.xy.decreasing = c(TRUE, TRUE),
  plot.font.size.base = 12,
  nodes.colour.seq = c("#00809D", "#EEEEEE", "#C30000"),
  nodes.colour.value.seq = c(0, 0.5, 1),
  nodes.size.range = c(2, 8),
  axis.text.x.pattern = element_text(angle = 30, hjust = 1)
)

Arguments

object	A InterCell object, which is created by CreateInterCellObject.
direction.X.to.Y	Options are 'NULL', 'TRUE', 'FALSE'. It selects subset of data based on direction. The 'NULL' will keep 2-way interacting pairs, 'TRUE' keeps the X-to-Y pairs and 'FALSE' keeps the Y-to-X pairs. See details for help.
bound.to.use	It specifies the user specified bound for evaluation params. The values out of bound will be coerced to either lower bound or upper bound. Default no bound is set, i.e. [-Inf, +Inf]
func.to.use	The function used to further transform the values, e.g. log1p.
plot.X.to.Y	The clusters drawn in x-axis and y-axis are in default aligned with the network analysis. If set FALSE, switch the clusters drawn in x-axis and y-axis.
axis.order.xy	It determines how the gene names will be ordered in the axis when plotting. Default is AlphaBet, options are Power and Confidence.
axis.order.xy.decreasing	It determines whether the orders are of decreasing pattern or increasing pattern.
plot.font.size.base	It gives the font size of texts such as labels and titles.
nodes.colour.seq	It specifies the colour sequence of the nodes.
nodes.colour.value.seq	It is along with the param nodes.colour.seq, and changes the colour expansion.
nodes.size.range	It specifies the size range of the nodes.
axis.text.x.pattern	It defines the axis text style in x-axis.

Details

The meaning for 2 used values is:

• LogFC: the log fold change, which indicates the relative gene expression.

• PVal: the confidence of discovering the gene as differently expressed genes. If it is generated from Seurat, it is orginally calculated by bonferroni correction.

Illustration for direction.X.to.Y: When running this function, gene pairs have been combined with their actions. As a result, gene pairs get to have direction for their action, e.g. IL6->IL6R, which means IL6 gets to activate IL6R, and the direction should be IL6 to IL6R. Suppose IL6 is expressed by cell cluster X, IL6R is expressed by cell cluster Y, then IL6->IL6R will be reserved if direction.X.to.Y is set either 'NULL' or 'TRUE', but not 'FALSE'. The cluster X and Y is aligned with what users specified in link{AnalyzeInterInFullView}, and X corresponds to those clusters shown in x-axis and Y corresponds to those in y-axis. More closely, the X and Y are corresponding to cluster.x and cluster.y given by FetchInterOI.

Value

List. Use Tool.ShowPlot() to see the plot, Tool.WriteTables() to save the result table in .csv files.

• plot: the object of ggplot2.

• table: a list of data.frame.

ZJUDBlab/InterCellDB documentation built on March 19, 2023, 4:56 p.m.