iplot {sparrow} | R Documentation

## Visualize gene level behavior of genes within a geneset across a contrast.

### Description

It is informative to look at the individual log fold changes of the genes within a gene set to explore the degree to which they (1) are coherent with respect to each other; and (2) see how the compare to the background distribution of log fold changes of the entire transcriptome.

You can visualize this behavior via a `type = "density"` plot, or a `type = "boxplot". It is also common to plot either the individual log fold changes` value = "logFC"`or t-statistics`value = "t"'.

### Usage

    iplot(
      x,
      name,
      value = "logFC",
      type = c("density", "gsea", "boxplot"),
      tools = c("wheel_zoom", "box_select", "reset", "save"),
      main = NULL,
      with.legend = TRUE,
      collection = NULL,
      shiny_source = "mggenes",
      width = NULL,
      height = NULL,
      ggtheme = ggplot2::theme_bw(),
      trim = 0.005,
      ...
    )

### Arguments

`x` | A `SparrowResult()` object
`name` | the name of the geneset to plot
`value` | A string indicating the column name for the value of the gene-level metadata to plot. Default is `"logFC"`. Anoter often used choice might also be `"t"`, to plot t-statistics (if they're in the result). But this can be any numeric column found in the data.frame returned by `geneSet(x, y, j)`. If this is a named string (vector), then the value in `names(value)` will be used on the axis when plotted.
`type` | plot the distributions as a `"density"` plot or `"boxplot"`.
`tools` | the tools to display in the rbokeh plot
`main` | A title to display. If not specified, the gene set name will be used, otherwise you can pass in a custom title, or `NULL` will disable the title altogether.
`with.legend` | Draws a legend to map point color to meaning. There are three levels a point (gene level statistic) can be color as, "notsig", "psig", and "sig". "notsig" implies that the FDR >= 10%, "psig" means that FDR <= 10%, but the logFC is "unremarkable" (< 1), and "sig" means that both the FDR <= 10% and the logFC >= 1
`collection` | If you have genesets with duplicate names in `x` (only possible with a `GeneSetDb` object), provide the name of the collection here to disambiguate (default: `NULL`).
`shiny_source` | the name of this element that is used in shiny callbacks. Defaults to `"mggenes"`.
`width, height` | the width and height of the output plotly plot
`ggtheme` | a ggplot theme, like the thing returned from `ggplot2::theme_bw()`, for instance.
`trim` | used to define the upper and lower quantiles to max out the individual gene statistics in the selected geneset.
`...` | pass through parameters to internal boxplot/density/gsea plotting functions

### Value

the ploty plot object

### Examples

    mgr <- exampleSparrowResult()
    iplot(mgr, "BURTON_ADIPOGENESIS_PEAK_AT_2HR",
          value = c("t-statistic" = "t"),
          type = "density")
    iplot(mgr, "BURTON_ADIPOGENESIS_PEAK_AT_2HR",
          value = c("log2FC" = "logFC"),
          type = "boxplot")
    iplot(mgr, "BURTON_ADIPOGENESIS_PEAK_AT_2HR",
          value = c("-statistic" = "t"),
          type = "gsea")

[Package sparrow version 1.0.3 Index]