reportgen: Generating ICA or PCA summary reports.

In jinhyunju/picaplot: An R package for analyzing gene expression data with Principal / Independent Component Analysis

Description

Generating a HTML report from a ICA or PCA list object.

Usage

reportgen(input_list = NULL, n_comps = NULL, prefix = NULL,
  geneinfo_df = NULL, output_path = NULL, file.ext = "png")

Arguments

input_list	ICA or PCA result list created by either runICA() or runPCA().
n_comps	Number of components to plot. Default is set to plot every component.
prefix	Output filename prefix. The output file will be named "prefix_PICA_summary.html".
geneinfo_df	Dataframe that contains positions of the genes. Column names should be "pheno_chr" for chromosomes, "pheno_start" for starting position and "pheno_end" for ending positions.
output_path	Directory path for generating the output HTML file. default is set to current working directory.
file.ext	File extension to be used for saved plots. Default is set to png for html reports. Note that if you use pdf plots for html files they will not show up in your report.

Value

The output of this function is a HTML report containing component-wise plots and information.

Examples

data(expr_data)

ica_result <- runICA(expr_data)
ica_result <- covarAssociationCheck(ica_result, sample_info)
ica_result <- detectClusters(ica_result)

reportgen(ica_result, geneinfo_df = probe_info, output_path = "./", prefix ="example_report")

jinhyunju/picaplot documentation built on May 19, 2019, 10:35 a.m.