visualizationBox: Generate a boxplot

In lootpiz/PatiDem: Characterization of PATIent DEMographics

Description

Generate a boxplot to compare a specific phenotype for a set of samples.

Usage

visualizationBox(
  object,
  cancer_type = NULL,
  patients = NULL,
  phenotype,
  metadata_col,
  metadata_levels
)

Arguments

object	matrix Patient information (matrix)
cancer_type	vector A vector of cancer types of interest from 'type' column
patients	vector A vector of patient barcodes from 'bcr_patient_barcode' column
phenotype	character A string of a specific phenotype (column name)
metadata_col	character A string of the column name (phenotype) to be split into groups
metadata_levels	vector A vector of two values (factors) to be compared

Value

None/plot a box plot

Author(s)

Heewon Seo, [e-mail]

Examples

tcga <- downloadData()

visualizationBox(tcga, cancer_type = c("BLCA", "BRCA"),
    phenotype = "age_at_initial_pathologic_diagnosis",
    metadata_col = "race", 
    metadata_levels = c("WHITE", "ASIAN"))

visualizationBox(tcga, cancer_type = c("BLCA", "BRCA"),
    phenotype = "age_at_initial_pathologic_diagnosis",
    metadata_col = "race", 
    metadata_levels = c("WHITE", "ASIAN", "BLACK OR AFRICAN AMERICAN"))

lootpiz/PatiDem documentation built on July 27, 2020, 12:35 a.m.