Heatmap trelliscope building function for RNA-seq data

Source: R/trelliPlots_seqData.R

Specify a plot design and cognostics for the RNA-seq heatmap trelliscope. Data must be grouped by an e_meta column. Main_effects order the y-variables. All statRes data is ignored. For MS/NMR data, use "trelli_abundance_heatmap".

trelli_rnaseq_heatmap(
  trelliData,
  cognostics = c("sample count", "mean LCPM", "biomolecule count"),
  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, and grouped by an emeta variable. Must be built using seqData. Required.

cognostics

A vector of cognostic options. Defaults are "sample count", "mean LCPM" and "biomolecule count". "sample count" and "mean LCPM" are reported per group, and "biomolecule count" is the total number of biomolecules in the biomolecule class (e_meta column).

ggplot_params

An optional vector of strings of ggplot parameters to the backend ggplot function. For example, c("ylab(”)", "xlab(”)"). Default is NULL.

interactive

A logical argument indicating whether the plots should be interactive or not. Interactive plots are ggplots piped to ggplotly. 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 heatmaps that is stored in `path`

Author

David Degnan, Lisa Bramer

Examples