inHeatmap {INSPEcT} | R Documentation

## Heatmap that represent the fold changes of all the five features

### Description

A method to see as an heatmap the logRatios of synthesis, degradation and processing rates and pre-RNA and total RNA concentration of a population of genes, either at the level of etimated or modeled rates.

### Usage

    inHeatmap(
      object,
      type = "pre-model",
      breaks = seq(-1, 1, length.out = 51),
      palette = colorRampPalette(c("green", "black", "firebrick3")),
      plot_matureRNA = FALSE,
      absoluteExpression = TRUE,
      show_rowLabels = TRUE,
      clustering = TRUE,
      clustIdx = 3:5
    )

    ## S4 method for signature 'INSPEcT'
    inHeatmap(
      object,
      type = "pre-model",
      breaks = seq(-1, 1, length.out = 51),
      palette = colorRampPalette(c("green", "black", "firebrick3")),
      plot_matureRNA = FALSE,
      absoluteExpression = TRUE,
      show_rowLabels = TRUE,
      clustering = TRUE,
      clustIdx = 3:5
    )

### Arguments

`object` | An object of class INSPEcT
`type` | Eiher "pre-model" or "model" to switch between pre-modeled or modeled features
`breaks` | A vector of breaks for the heatmap
`palette` | A color generating function, output of colorRampPalette
`plot_matureRNA` | A logical. If set to TRUE, matrue-RNA is displayed instead of total-RNA (default: FALSE)
`absoluteExpression` | A logical. If set to FALSE, the plot representing the intensity of expression is omitted. (default=TRUE)
`show_rowLabels` | A logical defining whether rownames are reported or not. (default=TRUE)
`clustering` | A logical. If set to FALSE, it displys genes the order they are, with no clustering (default: TRUE)
`clustIdx` | A numeric. Indicates which of the features are used for the clustering. 0=absoluteExpression; 1=total-RNA/mature-RNA; 2=preMRNA; 3=synthesis; 4=degradation; 5=processing (default=3:5, meaning that synthesis, degradation and processing are used for the clustering)

### Value

A list of matrices containing the logRatios for total RNA levels, pre-RNA levels, synthesis rates, degradation rates and processing rates. Matrices are ordered according to the clustering.

### Examples

    nascentInspObj10 <- readRDS(system.file(package='INSPEcT', 'nascentInspObj10.rds'))
    inHeatmap(nascentInspObj10, 'pre-model')
    inHeatmap(nascentInspObj10, 'model')

[Package INSPEcT version 1.20.0 Index]