GetResultTgSpecificity: Get Result for Specificity Analysis
In ZJUDBlab/InterCellDB: Tool and Database for Analyzing Interactions

GetResultTgSpecificity

R Documentation

Get Result for Specificity Analysis

Description

This function is to summary gene pair specificity by showing all gene pairs with their co-occurring interactions. Gene pairs are evaluated on both power and confidence like it in GetResultTgCrosstalk.

Usage

GetResultTgSpecificity(
  object,
  sel.uq.cnt.options = integer(),
  sel.gene.pairs = NULL,
  sel.gene.pairs.method = NULL,
  sel.by.method.count = 10,
  sel.by.method.decreasing = TRUE,
  prioritize.cluster.groups = character(),
  plot.name.X.to.Y = TRUE,
  plot.uq.cnt.merged = TRUE,
  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) }),
  grid.plot.ncol = 1,
  barplot.or.dotplot = FALSE,
  plot.font.size.base = 12,
  axis.text.x.pattern = element_text(angle = 90, vjust = 0.5, hjust = 1),
  bar.facet.scales = "free_x",
  bar.facet.space = "free_x",
  bar.facet.text.x = element_text(size = 8, colour = "black"),
  bar.facet.background = element_rect(fill = "lightgrey", colour = "white"),
  bar.colour = character(),
  bar.width = 0.8,
  dot.colour.seq = c("#00809D", "#EEEEEE", "#C30000"),
  dot.colour.value.seq = c(0, 0.5, 1),
  dot.size.range = c(2, 8),
  dot.y.order.in.alphabet = TRUE,
  ...
)

Arguments

`object`	A `InterCell` object, which is created by `CreateInterCellObject`.
`sel.uq.cnt.options`	It defines the range of co-occurence count to be shown in result. If no option is given, it will use all available co-occurence count.
`sel.gene.pairs`	Directly specify the desired gene pairs. It should be given in standard table that is generated by `FormatCustomGenePairs`. The order of gene pairs will be implicitly used for result graph and table. In addition, it's strictly aligned to clusters, which is illustrated in `AnalyzeInterInFullView`.
`sel.gene.pairs.method`	Options are: "random", "by-power" or not to use (by set NULL). It works only when no specific gene pairs are given in parameter `sel.gene.pairs`. Method "random" will randomly pick up some gene pairs. Method "by-power" will calculate the power of the 2 genes in every gene pairs, and order them by the calculated values. The order of gene pairs generated by method will be implicitly used for result graph and table.
`sel.by.method.count`	It defines the maximum number of gene pairs to be fetched by any method.
`sel.by.method.decreasing`	It works for method "by-power". If TRUE, result will be ordered in decreasing way, otherwise the increasing direction.
`prioritize.cluster.groups`	It defines the most concerning cluster groups, and those cluster groups given in this parameter, will be finally plotted from the most left-side to right.
`plot.name.X.to.Y`	If set FALSE, switch the position of 2 involving clusters in the original names of interaction. If set TRUE, keep still.
`plot.uq.cnt.merged`	If set TRUE, then gene pairs of different count of co-occurence will be merged to show in the result, or gene pairs will be grouped by their count of co-occurence and be plotted accordingly.
`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`.
`grid.plot.ncol`	It gives the number of columns for plotting grid when `plot.uq.cnt.merged = FALSE`.
`barplot.or.dotplot`	If TRUE, use 'barplot', or, use 'dotplot'.
`plot.font.size.base`	It defines the base font size for all texts.
`axis.text.x.pattern`	It defines the axis text style in x-axis.
`bar.facet.scales`	It controls the scales that facet uses, and gets 4 options as defined by ggplot2: "fixed", "free", "free_x", "free_y".
`bar.facet.space`	It controls the space allocating strategy that facet uses, and gets 4 options as defined by ggplot2: "fixed", "free", "free_x", "free_y".
`bar.facet.text.x`	It defines the style of facet text on the top horizontal position.
`bar.facet.background`	It defines the background style of labels among facets.
`bar.colour`	It gives colors that plotting bars get to use. If no specific colour is given, then the built-in 20 kinds of colours will be used.
`bar.width`	It defines the bar width.
`dot.colour.seq`	It specifies the colour sequence for dots.
`dot.colour.value.seq`	It is along with the param `dot.colour.seq`, and changes the colour expansion.
`dot.size.range`	It specifies the size range of the dots
`dot.y.order.in.alphabet`	If set TRUE, force to order gene pairs in alphabet, which ignores the implicit order by `sel.gene.pairs` or `sel.gene.pairs.method`.
`...`	Other parameter that can be passed to select by method functions.