Create a DT::datatable of feature level statistics for use in shiny bits — renderFeatureStatsDataTable • sparrow.shiny

We often want to display an interactive table of feature level statistics for all features. This function is a convenience wrapper to do that.

renderFeatureStatsDataTable(
  x,
  features = NULL,
  digits = 3,
  columns = NULL,
  feature.link.fn = NULL,
  order.by = "logFC",
  order.dir = c("desc", "asc"),
  filter = "none",
  length.opts = c(10, 25, 50, 100, 250)
)

Arguments

x: A `SparrowResult` or `data.frame` of feature level statistics. When `x` is a `SparrowResult`, the `logFC` feature level statistics will be extracted for display.
features: A character vector that specifies the subset of `feature_id`'s to display from `x`. If `NULL` (default), all of `x` will be used.
digits: number of digits to round the numeric columns to
columns: the columns from `x` to use. If `missing`, then only `c('symbol', 'feature_id', 'logFC', 'pval', 'padj', order.by)` will be used. If explicitly set to `NULL` all columns will be used.
feature.link.fn: A function that receives the data.frame of statistics to be rendered and transforms one of its columns into a hyperlink for further reference. Refer to [ncbi.entrez.link()] as an example.
order.by: name of the column to order the geneset stats by
order.dir: do we order the table by the values in `order.by` in `"desc"`-ending, or `"asc"`-ending order (default: `"desc"`)
filter: passed to [DT::datatable()]
length.opts: parameter passed as an option to [DT::datatable()] that specifies how long the table can be per page.

Value

A [DT::datatable()] of feature statistics

Examples

sr <- sparrow::exampleSparrowResult()
lfc <- sparrow::logFC(sr)
if (interactive()) {
  renderFeatureStatsDataTable(sr, sample(lfc$feature_id, 200),
                              feature.link.fn = ncbi.entrez.link)
}