Create_heatmap: Create a heatmap

In SPIDDOR/SPIDDOR: SPIDDOR

Description

Plot a heatmap of the perturbation analysis results.

Usage

Create_heatmap(M, hclust.method = "average", palette = NULL,sensitivity=0.2,...)

Arguments

M	Output matrix of the perturbation analysis results.
hclust.method	Hierarchical clustering method.
palette	Color palette to use in the heatmap. By default, the perturbations that lead to a higher activation of the nodes compared to an unperturbed situation are represented in orange while a lower activation of the nodes is indicated in blue.
sensitivity	Percentage of change of the attractors (perturbed situation vs baseline attractor) from which the cells of the heatmap start to be colored. By default, the function colors the heatmaps when changes in the attractor states are greater than 20% (sensitivity=0.2).
...	Extra arguments to pass to heatmap.2 function from gplots package

Value

A heatmap to visualize the individual values contained in the matrix returned by KO_matrix.f and OE_matrix.f as colors.

See Also

See Also KO_matrix.f OE_matrix.f

Examples

#Load the example network:
## Not run: 
 data(Example_network)
 #Read the Boolean functions:
 BN <- read.Boolean.functions(Lines=BN$BooleanFunctions)
 #Perturbation analysis: knockouts
 KO.m<-KO_matrix.f(BN,time.steps=999,repetitions=24,asynchronous=TRUE)
 #Create a heatmap of the results:
 Create_heatmap(KO.m)
 #In order to see the numeric values of each cell:
 Create_heatmap(KO.m,cellnote=round(KO.m,digits=2),notecol="white")
 
## End(Not run)

SPIDDOR/SPIDDOR documentation built on May 9, 2019, 11:42 a.m.