Clinical-class: Class Clinical

In griffithlab/GenVisR: Genomic Visualizations in R

Class Clinical

Description

An S4 class to store clinical information and plots, under development!!!

Usage

Clinical(
  path,
  inputData = NULL,
  inputFormat = c("wide", "long"),
  legendColumns = 1,
  palette = NULL,
  clinicalLayers = NULL,
  verbose = FALSE
)

Arguments

path	String specifying the path to clinical data, file must have the column "sample".
inputData	Optional data.table or data.frame object holding clinical data, used only if path is not specified. Data must have the column "sample".
inputFormat	String specifying the input format of the data given, one of wide or long format (see details).
legendColumns	Integer specifying the number of columns in the legend.
palette	Named character vector supplying colors for clinical variables.
clinicalLayers	list of ggplot2 layers to be passed to the plot.
verbose	Boolean specifying if progress should be reported.

Details

The Clinical() function is a constructor to create a GenVisR object of class Clinical. This is used to both display clinical data in the form of a heatmap and to add clinical data to various GenVisR plots. Input to this function can be either the path to a file containing clinical information using the parameter "path", or alternatively a data.table object if this information into R. By default the input is assumed to be in a wide format where each variable has it's own column, in such cases the data will be coerced into a long format where there is a key->value pair mapping to the data. The assumption of "wide"/"long" format can be changed with the "inputFormat" parameter, in both cases there should be a column called "sample" within the data supplied which is used as an id variable.

Slots

clinicalGrob

gtable object for the clinical plot.

clinicalLayers

list of ggtheme or ggproto objects used to build the plot.

clinicalData

data.table object to store clinical data

See Also

getData

drawPlot

griffithlab/GenVisR documentation built on May 14, 2024, 12:40 a.m.