Boxplot trelliscope building function for RNA-seq data

Source: R/trelliPlots_seqData.R

Specify a boxplot design and cognostics for the RNA-Seq boxplot trelliscope. Each boxplot will have its own groups as specified by the first main effect in group_designation. Use "trelli_abundance_boxplot" for MS/NMR-based omics.

trelli_rnaseq_boxplot(
  trelliData,
  cognostics = c("count", "mean lcpm"),
  ggplot_params = NULL,
  interactive = FALSE,
  include_points = TRUE,
  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 trelli_panel_by. Must be built using seqData. Required.

cognostics

A vector of cognostic options for each plot. Valid entries are "count", "mean lcpm", "median lcpm", and "cv lcpm". If data are paneled by a biomolecule, the count will be "sample count". If data are paneled by a sample or a biomolecule class, the count will be "biomolecule count". If statRes data is included, "p-value" and "fold change" data per comparisons may be added. If grouping information is included, only "sample count" and "mean lcpm" will be calculated, along with "p-value" and "fold change" if specified. "p-value" will not be included if paneling a trelliscope display by a biomolecule class. Default is "sample count" and "mean lcpm".

ggplot_params

An optional vector of strings of ggplot parameters to the backend ggplot function. For example, c("ylab('')", "ylim(c(2,20))"). 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.

include_points

Add points as a geom_jitter. Default is TRUE.

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 boxplots that is stored in `path`

Author

David Degnan, Lisa Bramer

Examples