inst/extdata/script.R

In RNaviCell: Visualization of High-Throughput Data on Large-Scale Biological Networks

# create NaviCell object
n <- NaviCell()

# create active NaviCell session with the server
n$launchBrowser()

#get path of data
file<-system.file("extdata", "DU145_data.txt", package = "RNaviCell")

# read in prostate expression data as R matrix 
mat <- n$readDatatable(file)

# import data into active NaviCell session
n$importDatatable("mRNA expression data", "DU145", mat)

# configure color and treshold parameters 
n$continuousConfigSwitchSampleTab("DU145", "color")
n$continuousConfigSetStepCount("sample", 'color', 'DU145', 2)
n$continuousConfigSetColorAt("DU145", "sample", 1, 'FFFFFF')
n$continuousConfigSetValueAt("DU145", "color", "sample", 0, -1)
n$continuousConfigSetValueAt("DU145", "color", "sample", 2, 1)
n$continuousConfigApply("DU145", "color")

# select map staining as graphical representation for prostate cancer data
# and show the results
n$mapStainingEditorSelectDatatable('DU145')
n$mapStainingEditorSelectSample('data')
n$mapStainingEditorApply()