inHeatmap {INSPEcT} | R Documentation |
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.
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 )
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) |
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.
nascentInspObj10 <- readRDS(system.file(package='INSPEcT', 'nascentInspObj10.rds')) inHeatmap(nascentInspObj10, 'pre-model') inHeatmap(nascentInspObj10, 'model')