PlotOnACSN: Project ROMA results onto ACSN maps

In Albluca/rRoma: An r implementation of ROMA

Description

Project ROMA results onto ACSN maps

Usage

PlotOnACSN(RomaData, SampleName, AggScoreFun = "mean", QTop = NULL,
  QBottom = NULL, MapURL = "", Selected = NULL, FilterByWei = NULL,
  AggGeneFun = "mean", DispMode = "Module", DataName = "Sample",
  DefDispVal = 0, PlotInfo = TRUE, ReturnInfo = FALSE,
  LocalRange = FALSE)

Arguments

RomaData	list, the analysis returned by rRoma
SampleName	vector, string. The name(s) of the sample to consider
AggScoreFun	string, scalar. The name of the aggregating function used to compute the valus of the gene score. Note that this function will be applied even to genes appearin in one geneset. To consider only genes found in a single module use the 'GetSingle' function and set DefDispVal to 0
QTop	numeric, scalar. The quantile threshold associted with the top saturation color. If NULL, the max will be used.
QBottom	numeric, scalar. The quantile threshold associted with the lower saturation color. If NULL, the min will be used.
MapURL	string, scalar. The url of the map to use. The available maps can be seen on acsn.curie.fr and navicell.curie.fr. Possible values include 'https://navicell.curie.fr/navicell/maps/cellcycle/master/index.php' 'https://acsn.curie.fr/navicell/maps/dnarepair/master/index.php' 'https://acsn.curie.fr/navicell/maps/emtcellmotility/master/index.php' 'https://navicell.curie.fr/navicell/maps/ewing/master/index.php' 'https://navicell.curie.fr/navicell/maps/dendcells/master/index.php'
Selected	vector, integer. The position of the genesets to plot
FilterByWei	scalar, number of median-absolute-deviations away from median variace of gene weights required for a value to be called an outlier and filtered. If NULL genes are not filtered.
AggGeneFun	string, scalar. The name of the function used to combine scored if multiple samples are considered
DispMode	string, vector. The quantity to be projected on the maps (in the form of an heatmap). It can be any combination of the following: 'Module': gene score is obtained by aggregating the score of selected modules containing that gene. The aggregating function is specified by the AggGeneFun parameter. 'Gene': gene score is obtained by aggregating the weigth of the genes across the selected modules. The aggregating function is specified by the AggGeneFun parameter.
DataName	string, scalar. The name of the dataset that will be reported in the web interface
DefDispVal	numeric, scalar. The value to be used when the fucntion defined by AggScoreFun produce NA (e.g., sd applied to genes that appear only in one geneset)
PlotInfo	boolean scalar. Should information plot be produced?
ReturnInfo	boolean scalar. Should information be returned?
LocalRange	boolean scalar. Should color bounds be relative to the considered samples only?

Albluca/rRoma documentation built on May 5, 2019, 1:35 p.m.