GetResultFullView: Get Result for Network Analysis

In ZJUDBlab/InterCellDB: Tool and Database for Analyzing Interactions

Get Result for Network Analysis

Description

This function summarizes the result of network analysis in graph and table, and gives clues to most active intercellular communications.

Usage

GetResultFullView(
  object,
  show.clusters.in.x = NULL,
  show.clusters.in.y = NULL,
  sel.cluster.group.method = "all",
  power.apply.func = NULL,
  cnt.apply.func = NULL,
  plot.power.range = NULL,
  plot.cnt.range = NULL,
  nodes.size.range = c(1, 6),
  nodes.colour.seq = c("#00809D", "#EEEEEE", "#C30000"),
  nodes.colour.value.seq = c(0, 0.5, 1),
  plot.axis.x.name = "clusters-x",
  plot.axis.y.name = "clusters-y"
)

Arguments

object	A InterCell object, which is created by CreateInterCellObject.
show.clusters.in.x	Clusters chosen to show in x-axis, corresponding to paramter sel.clusters.X in AnalyzeInterInFullView.
show.clusters.in.y	Clusters chosen to show in y-axis, corresponding to paramter sel.clusters.Y in AnalyzeInterInFullView.
sel.cluster.group.method	Options are 'all', 'diagonal' and 'diagonal-2'. It controls 'all' is recommended for most cases, and 'diagonal*' is recommended when same restrictions are applied to clusters in X and Y.
power.apply.func	The function used to modify the power value, usually log1p, etc.
cnt.apply.func	The function used to modify the count value, usually sqrt to avoid extremes problem.
plot.power.range	This will extend the plotting range beyond actual value range for power.
plot.cnt.range	This will extend the plotting range beyond actual value range for count.
nodes.size.range	2 numbers that specifies the range of sizes of the nodes shown in the graph.
nodes.colour.seq	Given colours will be used to generate colour gradient for plotting.
nodes.colour.value.seq	Numeric. If set NULL, colours given in nodes.colour.seq will be evenly placed. Otherwise, numeric values with the same length of nodes.colour.seq should be given to specify the positions corresponding to each colour. See parameter values in ggplot2::scale_colour_gradientn for details.
plot.axis.x.name	X-axis name when plotting.
plot.axis.y.name	Y-axis name when plotting.

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.