levi: levi

In levi: Landscape Expression Visualization Interface

Description

This is the Levi script mode. It allows you to create the integration of networks and gene expression levels as batch processing

Usage

levi(expressionInput, fileTypeInput, networkCoordinatesInput,
networkInteractionsInput, geneSymbolnput, readExpColumn,
contrastValueInput, zoomValueInput, resolutionValueInput,
smoothValueInput, expressionLog, contourLevi, setcolor)

Arguments

expressionInput	Filename of gene expression data, which is a numeric data.frame or matrix. The rows represent genes/proteins and the columns represent the experiment (RNA-seq, microarray, etc).
fileTypeInput	Filename of biological network. Levi can read files written in the following formats: Medusa (DAT), RedeR (DYN), Pajek (NET) and STRING/STITCH
networkCoordinatesInput	It allows the user to load the coordinate of the nodes the network.
networkInteractionsInput	Parameter available only to STRING/STITCH data format. It allows the user to load the interaction data file of the network.
geneSymbolnput	Column name from gene expression data containing the identifier (gene Symbol, Entrez ID, EMSEMBL, etc).
readExpColumn	Variable from readExpColumn function containing the comparisons of the experiments
contrastValueInput	Numeric value for image contrast. The variable range is 0 to 100. The default value is 50
zoomValueInput	Numeric value for image zoom. The variable range is 0 to 100. The default value is 50.
resolutionValueInput	Numeric value for image resolution. The variable range is 0 to 100. The default value is 50.
smoothValueInput	Numeric value for image smoothness. The variable range is 0 to 100. The default is 50.
expressionLog	Logical variable to indicate Log2 normalization in the expression levels. The default is FALSE
contourLevi	Logical variable to allow contour lines. The default is TRUE.
setcolor	Select the color palette to build the heatmat. There is two options the Multicolor has 20 color levels combined. The Two colors has two types of color and the options available are: purple\_pink, green\_blue, blue\_yellow, pink\_green, orange\_purple, green\_marine.

Details

Integrates the biological network and gene expression levels (or other type of data)

Value

Return a ggplot object and print a image (heatmat).

Author(s)

Isabelle Mira da Silva ([e-mail]), Jos<c3><a9> Rafael Pilan ([e-mail])

Examples

template_network <- file.path(system.file(package="levi"),"extdata",
   "medusa.dat", fsep = .Platform$file.sep)

template_expression <- file.path(system.file(package="levi"),
   "extdata","expression.dat", fsep = .Platform$file.sep)

multicolor <- levi(networkCoordinatesInput = template_network,
   expressionInput = template_expression, fileTypeInput = "dat",
   geneSymbolnput = "ID",
   readExpColumn=readExpColumn("TumorCurrentSmoker-NormalNeverSmoker"),
   contrastValueInput = 50, resolutionValueInput  = 50, zoomValueInput = 50,
   smoothValueInput = 50, expressionLog = FALSE, contourLevi = TRUE)

twocolors <- levi(networkCoordinatesInput = template_network,
   expressionInput = template_expression, fileTypeInput = "dat",
   geneSymbolnput = "ID",
   readExpColumn = readExpColumn("TumorCurrentSmoker-NormalNeverSmoker"),
   setcolor = "pink_green", contourLevi = FALSE)

levi documentation built on Nov. 8, 2020, 8:21 p.m.