createReport: Generating SPADEVizR reports

In tchitchek-lab/SPADEVizR: SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results

Generating SPADEVizR reports

Description

Generates a customizable PDF report based on SPADEVizR visualization features.

Usage

createReport(Results, PDFfile = "report.pdf", select.plots = c("count",
  "heatmap", "MDSclusters", "pheno"), clusters = NULL, markers = NULL,
  samples = NULL, stat.objects = list(), width = 30, height = 10,
  verbose = TRUE)

Arguments

Results	a 'Results' object
PDFfile	a character specifying the output path
select.plots	a vector combining character and stat objects ('AC', 'DAC', 'CC' and 'AP') specifying the order of the desired plots (see details)
clusters	a character vector of clusters to include in the report (all will be included by default)
markers	a character vector of markers to include in the report (all will be included by default)
samples	a character vector providing the sample names to used (all samples by default)
stat.objects	a list containing one or several AC, DEC, CC or AP objects to plot in the report
width	a numeric specifying the width of the PDF file
height	a numeric specifying the height of the PDF file
verbose	a boolean specifying if some messages must be displayed during the generation of the report

Details

Available plots are :

• "count" (included by default):Displays a Count Viewer representation;

• "tree":Displays a SPADE Tree Viewer representation;

• "heatmap" (included by default):Displays an Heatmap Viewer representation;

• "boxplot":Displays a Boxplot Viewer representation;

• "kinetics":Displays a Kinetic Viewer representation;

• "streamgraph":Display a Streamgraph Viewer representation;

• "pheno" (included by default):Displays a Pheno Viewer representation;

• "MDSclusters" (included by default):Displays a MDS Viewer representation at the cluster level

• "MDSsamples":Displays a MDS Viewer representation at the sample level

• "distogram":Displays a Distogram Viewer representation;

• "kinetics_pheno":Displays two "kinetics" and "cluster" representations juxtaposed (one on the side of the other) for each cluster;

• "boxplot_pheno":Displays two "boxplot" and "cluster" representations juxtaposed (one on the side of the other) for each cluster;

• AC, DAC, CC and AP objects

Value

none

tchitchek-lab/SPADEVizR documentation built on Jan. 27, 2024, 8:58 p.m.