dResidualPlot {DepecheR} | R Documentation

## Showing the residuals when subtracting the values from one group from another on a SNE plot

### Description

This function is used to visually compare groups of individuals from whom comparable cytometry or other complex data has been generated, but where the number of individuals does not permit any statistical comparisons.

### Usage

    dResidualPlot(
      xYData,
      groupVector,
      clusterVector,
      densContour = TRUE,
      groupName1 = unique(groupVector)[1],
      groupName2 = unique(groupVector)[2],
      plotName = "default",
      title = FALSE,
      maxAbsPlottingValues,
      bandColor = "black",
      plotDir = ".",
      dotSize = 400/sqrt(nrow(xYData)),
      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.
`clusterVector` | Vector with the same length as xYData containing information about the cluster identity of each observation.
`densContour` | If density contours should be created for the plot(s) or not. Defaults to TRUE.
`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.
`maxAbsPlottingValues` | If multiple plots should be compared, it might be useful to define a similar color scale for all plots, so that the same color always means the same value. Such a value can be added here. It defaults to the maximum Wilcoxon statistic that is generated in the analysis.
`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.
`createOutput` | For testing purposes. Defaults to TRUE. If FALSE, no plots are generated.

### Value

A sne based plot showing which events that belong to a cluster dominated by the first or the second group.

### See Also

`dColorPlot`, `dDensityPlot`, `dWilcox`

### Examples

    # Load some data
    data(testData)
    ## Not run:
    # Load or create the dimensions that you want to plot the result over.
    # uwot::umap recommended due to speed, but tSNE or other method would
    # work as fine.
    data(testDataSNE)

    # Run the clustering function. For more rapid example execution,
    # a depeche clustering of the data is inluded
    # testDataDepeche <- depeche(testData[,2:15])
    data(testDataDepeche)

    # And finally run the function
    dResidualPlot(
        xYData = testDataSNE$Y, groupVector = testData[, 16],
        clusterVector = testDataDepeche$clusterVector
    )

    ## End(Not run)

[Package DepecheR version 1.10.0 Index]