esetPlotWrapper {esetVis} | R Documentation |
Wrapper function used for all plots of the visualizations contained in the package.
esetPlotWrapper(dataPlotSamples, dataPlotGenes = data.frame(), esetUsed, xlab = "", ylab = "", colorVar = character(0), color = if (length(colorVar) == 0) "black" else character(0), shapeVar = character(0), shape = if (length(shapeVar) == 0) 15 else numeric(0), sizeVar = character(0), size = if (length(sizeVar) == 0) { ifelse(typePlot == "interactive" && length(packageInteractivity) == 1 && packageInteractivity == "rbokeh", 5, 2.5) } else { numeric() }, sizeRange = numeric(0), alphaVar = character(0), alpha = if (length(alphaVar) == 0) 1 else numeric(0), alphaRange = numeric(0), title = "", symmetryAxes = c("combine", "separate", "none"), cloudGenes = TRUE, cloudGenesColor = "black", cloudGenesNBins = if (nrow(dataPlotGenes) > 0) sqrt(nrow(dataPlotGenes)) else numeric(), cloudGenesIncludeLegend = FALSE, cloudGenesTitleLegend = "nGenes", packageTextLabel = c("ggrepel", "ggplot2"), topGenes = 10, topGenesCex = 2.5, topGenesVar = character(0), topGenesJust = c(0.5, 0.5), topGenesColor = "black", topSamples = 10, topSamplesCex = 2.5, topSamplesVar = character(0), topSamplesJust = c(0.5, 0.5), topSamplesColor = "black", geneSets = list(), geneSetsVar = character(0), geneSetsMaxNChar = numeric(0), topGeneSets = 10, topGeneSetsCex = 2.5, topGeneSetsJust = c(0.5, 0.5), topGeneSetsColor = "black", includeLegend = TRUE, includeLineOrigin = TRUE, typePlot = c("static", "interactive"), figInteractiveSize = c(600, 400), ggvisAdjustLegend = TRUE, interactiveTooltip = TRUE, interactiveTooltipExtraVars = character(0), packageInteractivity = c("rbokeh", "ggvis"), returnTopElements = FALSE, returnEsetPlot = FALSE)
dataPlotSamples |
data.frame with columns 'X', 'Y' with coordinates
for the samples and with rownames which
should correspond and be in the same order as the sampleNames of
|
dataPlotGenes |
data.frame with two columns 'X' and 'Y' with coordinates for the genes |
esetUsed |
expressionSet (or SummarizedExperiment) object with data |
xlab |
label for the x axis |
ylab |
label for the y axis |
colorVar |
name of variable (in varLabels of the |
color |
character or factor with specified color(s) for the points,
replicated if needed. This is used only if |
shapeVar |
name of variable (in varLabels of the |
shape |
character or factor with specified shape(s) (pch) for the points,
replicated if needed. This is used only if |
sizeVar |
name of variable (in varLabels of the |
size |
character or factor with specified size(s) (cex) for the points,
replicated if needed.
This is used only if |
sizeRange, |
size (cex) range used in the plot, possible only
if the |
alphaVar |
name of variable (in varLabels of the |
alpha |
character or factor with specified transparency(s) for the points,
replicated if needed. This is used only if |
alphaRange |
transparency (alpha) range used in the plot,
possible only if the |
title |
plot title, ” by default |
symmetryAxes |
set symmetry for axes, either:
|
cloudGenes |
logical, if TRUE (by default), include the cloud of genes in the plot |
cloudGenesColor |
if |
cloudGenesNBins |
number of bins to used for the clouds of genes, by default the square root of the number of genes |
cloudGenesIncludeLegend |
logical, if TRUE (FALSE by default) include the legend for the cloud of genes (in the top position if multiple legends) |
cloudGenesTitleLegend |
string with title for the legend for the cloud of genes 'nGenes' by default |
packageTextLabel |
package used to label the outlying genes/samples/gene sets,
either |
topGenes |
numeric indicating which percentile (if <1) or number (if >=1) of genes most distant to the origin of the plot to annotate, by default: 10 genes are selected If no genes should be annotated, set this parameter to 0 Currently only available for static plot. |
topGenesCex |
cex for gene annotation (used when |
topGenesVar |
variable of the featureData used to label the genes,
by default: empty, the featureNames are used for labelling (used when |
topGenesJust |
text justification for the genes
(used when |
topGenesColor |
text color for the genes
(used when |
topSamples |
numeric indicating which percentile (if <1) or number (if >=1) of samples most distant to the origin of the plot to annotate, by default: 10 samples are selected If no samples should be annotated, set this parameter to 0. Currently available for static plot. |
topSamplesCex |
cex for sample annotation (used when |
topSamplesVar |
variable of the phenoData used to label the samples,
by default: empty, the sampleNames are used for labelling
(used when |
topSamplesJust |
text justification for the samples
(used when |
topSamplesColor |
text color for the samples
(used when |
geneSets |
list of gene sets/pathways, each containing
identifiers of genes contained in the set.
E.g. pathways from Gene Ontology databases output from the
|
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
Only used when |
geneSetsMaxNChar |
maximum number of characters for pathway names,
by default keep entire names
Only used when |
topGeneSets |
numeric indicating which percentile (if <=1) or number (if >1) of gene sets
most distant to the origin of the plot to annotate, by default: 10 gene sets are selected
If no gene sets should be annotated, set this parameter to 0.
Currently available for static plot.
Only used when |
topGeneSetsCex |
cex for gene sets annotation
Only used when |
topGeneSetsJust |
text justification for the gene sets
by default: c(0.5, 0.5) so centered
Only used when |
topGeneSetsColor |
color for the gene sets
(used when |
includeLegend |
logical if TRUE (by default) include a legend, otherwise not |
includeLineOrigin |
if TRUE (by default) include vertical line at x = 0 and horizontal line at y = 0 |
typePlot |
type of the plot returned, either 'static' (static) or interactive' (potentially interactive) |
figInteractiveSize |
vector containing the size of the interactive plot,
as [width, height]
by default: c(600, 400). This is passed to the
|
ggvisAdjustLegend |
logical, if TRUE (by default) adjust the legends in |
interactiveTooltip |
logical, if TRUE, add hoover functionality showing sample annotation (variables used in the plot) in the plot |
interactiveTooltipExtraVars |
name of extra variable(s)
(in varLabels of the |
packageInteractivity |
if |
returnTopElements |
logical, if TRUE return also the top elements |
returnEsetPlot |
logical, if TRUE return also the esetPlot object |
if typePlot
is:
static
:
if returnTopElements
is TRUE, and top elements can be displayed, a list with:
'topElements': the top elements labelled in the plot
'plot': the ggplot
object
otherwise, the ggplot
object only
interactive
: a ggvis
or rbokeh
object, depending on the packageInteractivity
parameter
Laure Cougnaud
library(ALL) data(ALL) ## run one spectral map analysis # create custom color palette colorPalette <- c("dodgerblue", colorRampPalette(c("white","dodgerblue2", "darkblue"))(5)[-1], "red", colorRampPalette(c("white", "red3", "darkred"))(5)[-1]) # run the analysis # with 'returnAnalysis' set to TRUE to have all objects required for the esetPlotWrapper outputEsetSPM <- esetSpectralMap(eset = ALL, title = "Acute lymphoblastic leukemia dataset \n Spectral map complete", colorVar = "BT", color = colorPalette, shapeVar = "sex", shape = 15:16, sizeVar = "age", sizeRange = c(2, 6), symmetryAxes = "separate", topGenes = 10, topGenesJust = c(1, 0), topGenesCex = 2, topGenesColor = "darkgrey", topSamples = 15, topSamplesVar = "cod", topSamplesColor = "black", topSamplesJust = c(1, 0), topSamplesCex = 3, returnAnalysis = TRUE) # plot the biplot print(outputEsetSPM$plot) ## re-call the plot function, to change some visualizations parameters esetPlotWrapper( dataPlotSamples = outputEsetSPM$analysis$dataPlotSamples, dataPlotGenes = outputEsetSPM$analysis$dataPlotGenes, esetUsed = outputEsetSPM$analysis$esetUsed, title = paste("Acute lymphoblastic leukemia dataset \n Spectral map"), colorVar = "BT", color = colorPalette, shapeVar = "relapse", sizeVar = "age", sizeRange = c(2, 6), topSamplesVar = "cod", topGenesVar = "SYMBOL" )