Histogram trelliscope building function for RNA-Seq data

Source: R/trelliPlots_seqData.R

Specify a plot design and cognostics for the abundance histogram trelliscope. Main_effects grouping are ignored. Data must be grouped by edata_cname. For MS/NMR data, use "trelli_abundance_histogram".

trelli_rnaseq_histogram(
  trelliData,
  cognostics = c("sample count", "mean lcpm", "median lcpm", "cv lcpm", "skew lcpm"),
  ggplot_params = NULL,
  interactive = FALSE,
  path = .getDownloadsFolder(),
  name = "Trelliscope",
  test_mode = FALSE,
  test_example = 1,
  single_plot = FALSE,
  ...
)

Arguments

trelliData

A trelliscope data object made by as.trelliData or as.trelliData.edata, and grouped by edata_cname in trelli_panel_by. Must be built using seqData. Required.

cognostics

A vector of cognostic options for each plot. Valid entries are "sample count", "mean lcpm", "median lcpm", "cv lcpm", and "skew lcpm". All are included by default.

ggplot_params

An optional vector of strings of ggplot parameters to the backend ggplot function. For example, c("ylab('')", "ylim(c(1,2))"). Default is NULL.

interactive

A logical argument indicating whether the plots should be interactive or not. Interactive plots are ggplots piped to ggplotly (for now). Default is FALSE.

path

The base directory of the trelliscope application. Default is Downloads.

name

The name of the display. Default is Trelliscope.

test_mode

A logical to return a smaller trelliscope to confirm plot and design. Default is FALSE.

test_example

A vector of plot indices to return for test_mode. Default is 1.

single_plot

A TRUE/FALSE to indicate whether 1 plot (not a trelliscope) should be returned. Default is FALSE.

...

Additional arguments to be passed on to the trelli builder

Value

No return value, builds a trelliscope display of histograms that is stored in `path`

Author

David Degnan, Lisa Bramer

Examples