groupProbPlot: Define and plot group probabilities

In Theorell/DepecheR: Determination of essential phenotypic elements of clusters in high-dimensional entities

Define and plot group probabilities

Description

This function defines and plots the single-observation probability for belonging to either of two groups. It uses the neighSmooth function with the special case that the values are binary: For each set of k nearest neighbors, cell x is assigned a probability to belong to one group or the other based on the percentage of the neighbors belonging to each group. In other words, if 20 out of 100 neighbors belong to group A and 80 belong to group B, and the value for the cell will be 20 A or 80 accordingly reflected in the color scale on the resulting plot.

Usage

groupProbPlot(
  xYData,
  groupVector,
  euclidSpaceData,
  kNeighK = max(100, round(nrow(euclidSpaceData)/10000)),
  kMeansK = round(nrow(euclidSpaceData)/1000),
  densContour = TRUE,
  groupName1 = unique(groupVector)[1],
  groupName2 = unique(groupVector)[2],
  plotName = "default",
  title = FALSE,
  bandColor = "black",
  plotDir = ".",
  dotSize = 400/sqrt(nrow(xYData)),
  returnProb = FALSE,
  returnProbColVec = FALSE,
  createOutput = TRUE
)

Arguments

xYData	A dataframe or matrix with two columns. Each row contains information about the x and y positition in the field for that observation.
groupVector	Vector with the same length as xYData containing information about the group identity of each observation.
euclidSpaceData	The data cloud in which the nearest neighbors for the events should be identified.
kNeighK	The number of nearest neighbors.
kMeansK	The number of clusters in the initial step of the algorithm. A higher number leads to shorter runtime, but potentially lower accuracy.
densContour	If density contours should be created for the plot(s) or not. Defaults to TRUE. a
groupName1	The name for the first group
groupName2	The name for the second group
plotName	The main name for the graph and the analysis.
title	If there should be a title displayed on the plotting field. As the plotting field is saved as a png, this title cannot be removed as an object afterwards, as it is saved as coloured pixels. To simplify usage for publication, the default is FALSE, as the files are still named, eventhough no title appears on the plot.
bandColor	The color of the contour bands. Defaults to black.
plotDir	If different from the current directory. If specified and non-existent, the function creates it. If "." is specified, the plots will be saved at the current directory.
dotSize	Simply the size of the dots. The default makes the dots smaller the more observations that are included.
returnProb	Should a probability vector be returned? Mutually exclusive with returnProbColVec.
returnProbColVec	Should the color vector be returned as part of the output? Mutually exclusive with returnProb.
createOutput	For testing purposes. Defaults to TRUE. If FALSE, no output is generated.

Value

A graph showing the probability as a color scale from blue over white to red for each event to belong to one group or the other, with a separate color scale. Optionally also the color vector, if returnProbColVec is TRUE.

Examples

data(testData)
data(testDataSNE)
euclidSpaceData <-
    testData[, c(
        "SYK", "CD16", "CD57", "EAT.2",
        "CD8", "NKG2C", "CD2", "CD56"
    )]
## Not run: 
groupProbPlot(
    xYData = testDataSNE$Y, groupVector = testData$label,
    euclidSpaceData
)

## End(Not run)

Theorell/DepecheR documentation built on July 27, 2023, 8:13 p.m.