plotInfReps {fishpond} | R Documentation

## Plot inferential replicates for a gene or transcript

### Description

For datasets with inferential replicates, boxplots are drawn for the two groups and potentially grouped by covariates. For datasets with only mean and variance, points and intervals (95 approximation) are drawn.

### Usage

    plotInfReps(
      y,
      idx,
      x,
      cov = NULL,
      colsDrk = c("dodgerblue", "goldenrod4", "royalblue4", "red3", "purple4", "darkgreen"),
      colsLgt = c("lightblue1", "goldenrod1", "royalblue1", "salmon1", "orchid1",
        "limegreen"),
      xaxis,
      xlab,
      ylim,
      main,
      mainCol,
      legend = FALSE,
      legendPos = "topleft",
      legendTitle = FALSE,
      legendCex = 1,
      useMean = TRUE,
      applySF = FALSE,
      reorder,
      thin
    )

### Arguments

`y` | a SummarizedExperiment (see `swish`)
`idx` | the name or row number of the gene or transcript
`x` | the name of the condition variable for splitting and coloring the samples or cells. Also can be a numeric, e.g. pseudotime, in which case, `cov` can be used to designate groups for coloring
`cov` | the name of the covariate for adjustment
`colsDrk` | dark colors for the lines of the boxes
`colsLgt` | light colors for the inside of the boxes
`xaxis` | logical, whether to label the sample numbers. default is `TRUE` if there are less than 30 samples
`xlab` | the x-axis label
`ylim` | y limits
`main` | title
`mainCol` | name of metadata column to use for title (instead of rowname)
`legend` | logical, show simple legend (default FALSE)
`legendPos` | character, position of the legend (default "topleft")
`legendTitle` | logical, whether to add the name of the grouping variable as a title on the legend (default FALSE)
`legendCex` | numeric, size of the legend (default 1)
`useMean` | logical, when inferential replicates are not present, use the `mean` assay or the `counts` assay for plotting
`applySF` | logical, when inferential replicates are not present, should `y$sizeFactor` be divided out from the mean and interval plots (default FALSE)
`reorder` | logical, should points within a group defined by condition and covariate be re-ordered by their count value (default is FALSE, except for alevin data)
`thin` | integer, should the mean and interval lines be drawn thin (the default switches from 0 [not thin] to 1 [thinner] at n=150 cells, and from 1 [thinner] to 2 [thinnest] at n=400 cells)

### Value

nothing, a plot is displayed

### Examples

    y <- makeSimSwishData()
    plotInfReps(y, 3, "condition")

    y <- makeSimSwishData(n=40)
    y$batch <- factor(rep(c(1,2,3,1,2,3),c(5,10,5,5,10,5)))
    plotInfReps(y, 3, "condition", "batch")

[Package fishpond version 1.8.0 Index]