Clinical-class {GenVisR} | R Documentation

## 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`

[Package GenVisR version 1.12.1 Index]