Prediction map

Description

This method is used to visualize the prediction heat-map. The prediction map is generated by mapping a color code on the ratio of the fitted values.

Usage

plotPredMap(object)

Arguments

Details

This method firstly interpolate the SQUAD Simulation Result. Then, it performs a ratio at a user-defined time point. Finally, a color code is assigned to the ratio value. The darker the color, the higher the increase of the node activation.

Author(s)

Martial Sankar

See Also

More information about heatmap, heatmap More specific information in plotPredMap-methods. For more informations about the input object see SquadSimResServiceImpl-class.

Examples

fpath <- system.file("extdata", package="SQUADD")
fileModel <- file.path(fpath,"data_IAA")
nm <- c("ARF(a)", "ARF(i)", "AR_Genes", "Aux/IAA", "BES1/BZR1",
 "BIN2", "BR", "BRI1-BAK1","BRR_Genes","BRX","BR_Biosynthesis",  "BZR1", "DO",
  "IAA", "IAA_Biosynthesis",   "NGA1", "PIN", "SCFTir1","StimAux", "StimBR")
t <- 50

## call constructor
obj <- simResService(
		folder=fileModel,
		time=t,
		ncolor=5,
		legend=nm,
		indexDeno=1,
		method="lowess")

## Apply method 
plotPredMap(obj)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(SQUADD)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SQUADD/plotPredMap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotPredMap
> ### Title: Prediction map
> ### Aliases: plotPredMap
> ### Keywords: prediction heatmap
> 
> ### ** Examples
> 
> fpath <- system.file("extdata", package="SQUADD")
> fileModel <- file.path(fpath,"data_IAA")
> nm <- c("ARF(a)", "ARF(i)", "AR_Genes", "Aux/IAA", "BES1/BZR1",
+  "BIN2", "BR", "BRI1-BAK1","BRR_Genes","BRX","BR_Biosynthesis",  "BZR1", "DO",
+   "IAA", "IAA_Biosynthesis",   "NGA1", "PIN", "SCFTir1","StimAux", "StimBR")
> t <- 50
> 
> ## call constructor
> obj <- simResService(
+ 		folder=fileModel,
+ 		time=t,
+ 		ncolor=5,
+ 		legend=nm,
+ 		indexDeno=1,
+ 		method="lowess")
> 
> ## Apply method 
> plotPredMap(obj)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>