INSPEcT (version 1.2.2)

inHeatmap: Heatmap that represent the fold changes of all the five features

Description

Heatmap that represent the fold changes of all the five features

A method to see as an heatmap the logRatios of synthesis, degradation and processing rates and pre-mRNA and total mRNA 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, rowLabels = NULL, clustering = TRUE, clustIdx = 3:5)
"inHeatmap"(object, type = "pre-model", breaks = seq(-1, 1, length.out = 51), palette = colorRampPalette(c("green", "black", "firebrick3")), plot_matureRNA = FALSE, absoluteExpression = TRUE, rowLabels = NULL, 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-mRNA is displayed instead of total-mRNA (default: FALSE)

absoluteExpression

A logical. If set to FALSE, the plot representing the intensity of expression is omitted. (default=TRUE)

rowLabels

A character that represent the label names that will be shown on the y-axis of the heatmap. If NULL featureNames(object) will be shown (default is NULL)

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-mRNA/mature-mRNA; 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 mRNA levels, pre-mRNA levels, synthesis rates, degradation rates and processing rates. Matrices are ordered according to the clustering.

Examples

data('mycerIds10', package='INSPEcT')
inHeatmap(mycerIds10, 'pre-model')
inHeatmap(mycerIds10, 'model')