plotSmoothers {tradeSeq} | R Documentation

## Plot the log-transformed counts and the fitted values for a particular gene along all lineages

### Description

Plot the smoothers estimated by `tradeSeq`.

### Usage

    plotSmoothers(models, ...)

    ## S4 method for signature 'gam'
    plotSmoothers(
      models,
      nPoints = 100,
      lwd = 2,
      size = 2/3,
      xlab = "Pseudotime",
      ylab = "Log(expression + 1)",
      border = TRUE,
      alpha = 1,
      sample = 1
    )

    ## S4 method for signature 'SingleCellExperiment'
    plotSmoothers(
      models,
      counts,
      gene,
      nPoints = 100,
      lwd = 2,
      size = 2/3,
      xlab = "Pseudotime",
      ylab = "Log(expression + 1)",
      border = TRUE,
      alpha = 1,
      sample = 1,
      pointCol = NULL
    )

### Arguments

`models` | Either the `SingleCellExperiment` object obtained after running `fitGAM`, or the specific GAM model for the corresponding gene, if working with the list output of `tradeSeq`.
`...` | parameters including:
`nPoints` | The number of points used to extraplolate the fit. Defaults to 100.
`lwd` | Line width of the smoother. Passed to `geom_line`.
`size` | Character expansion of the data points. Passed to `geom_point`.
`xlab` | x-axis label. Passed to `labs`.
`ylab` | y-axis label. Passed to `labs`.
`border` | Logical: should a white border be drawn around the mean smoother.
`alpha` | Numeric between 0 and 1, determines the transparancy of data points, see `scale_color_viridis_d`.
`sample` | Numeric between 0 and 1, use to subsample the cells when there are too many so that it can plot faster.
`counts` | The matrix of gene expression counts.
`gene` | Gene name or row in count matrix of gene to plot.
`pointCol` | Plotting colors for each cell. Can be either character vector of length 1, denoting a variable in the `colData(models)` to color cells by, or a vector of length equal to the number of cells.

### Value

A `ggplot` object

### Examples

    data(gamList, package = "tradeSeq")
    plotSmoothers(gamList[[4]])

[Package tradeSeq version 1.3.13 Index]