plotDEGRegression {singleCellTK} | R Documentation

## plot the linear regression to show visualize the expression the of DEGs identified by differential expression analysis

### Description

plot the linear regression to show visualize the expression the of DEGs identified by differential expression analysis

### Usage

    plotDEGRegression(
      inSCE,
      useResult,
      threshP = FALSE,
      labelBy = NULL,
      nrow = 6,
      ncol = 6,
      defaultTheme = TRUE,
      isLogged = TRUE,
      check_sanity = TRUE
    )

### Arguments

`inSCE` | SingleCellExperiment inherited object. `runMAST()` has to be run in advance.
`useResult` | character. A string specifying the `analysisName` used when running a differential expression analysis function.
`threshP` | logical. Whether to plot threshold values from adaptive thresholding, instead of using the assay used by `runMAST()`. Default `FALSE`.
`labelBy` | A single character for a column of `rowData(inSCE)` as where to search for the labeling text. Default `NULL`.
`nrow` | Integer. Number of rows in the plot grid. Default `6`.
`ncol` | Integer. Number of columns in the plot grid. Default `6`.
`defaultTheme` | Logical scalar. Whether to use default SCTK theme in ggplot. Default `TRUE`.
`isLogged` | Logical scalar. Whether the assay used for the analysis is logged. If not, will do a `log(assay + 1)` transformation. Default `TRUE`.
`check_sanity` | Logical scalar. Whether to perform MAST's sanity check to see if the counts are logged. Default `TRUE`

### Value

A ggplot object of linear regression

### Examples

    data("sceBatches")
    logcounts(sceBatches) <- log(counts(sceBatches) + 1)
    sce.w <- subsetSCECols(sceBatches, colData = "batch == 'w'")
    sce.w <- runWilcox(sce.w, class = "cell_type", classGroup1 = "alpha",
                       groupName1 = "w.alpha", groupName2 = "w.beta",
                       analysisName = "w.aVSb")
    plotDEGRegression(sce.w, "w.aVSb")

[Package singleCellTK version 2.2.0 Index]