plotTopElements: create 'geom_text' object with top genes/sample/pathways

Description Usage Arguments Value Author(s)

View source: R/plotTopElements.R

Description

create geom_text object with top genes/sample/pathways

Usage

1
2
3
4
5
6
plotTopElements(top, type = c("gene", "sample", "geneSets"),
  var = character(), cex = 1, just = c(0.5, 0.5), color = "black",
  dataPlotGenes = data.frame(), dataPlotSamples = data.frame(),
  esetUsed, geneSets = list(), geneSetsVar = character(),
  geneSetsMaxNChar = numeric(), returnTopElements = FALSE,
  packageTextLabel = c("ggrepel", "ggplot2"))

Arguments

top

numeric, number of top elements

type

type of elements to plot, either 'gene', 'sample', or 'geneSets'

var

variable used to annotate the elements, only used for 'gene' and 'sample'

cex

cex of text in the plot

just

justification of elements in the plot, only use if packageTextLabel is 'ggplot2'

color

color for the elements in the plot

dataPlotGenes

data.frame with two columns 'X' and 'Y' with coordinates for the genes

dataPlotSamples

data.frame with two columns 'X' and 'Y' with coordinates for the samples

esetUsed

expressionSet (or SummarizedExperiment) object with data

geneSets

list of gene sets, e.g. gene pathways, output from the 'getGeneSets' function in MLP the genes IDs must correspond to the sampleNames in the eset. If several gene sets have the same name, they will be combine to extract the top gene sets.

geneSetsVar

variable of the featureData used to match the genes contained in geneSets, most probably ENTREZID, if not specified the featureNames of the eSet are used

geneSetsMaxNChar

maximum number of characters for pathway names, by default keep entire names

returnTopElements

logical if TRUE (FALSE by default) return the outlying elements

packageTextLabel

package used to label the outlying genes/samples/gene sets, either 'ggrepel' (by default, only used if package ggrepel is available), or 'ggplot2'

Value

Author(s)

Laure Cougnaud


esetVis documentation built on Nov. 1, 2018, 4:30 a.m.