plottingFunctions: Convert clusterLegend into useful formats

Description Usage Arguments Format Details Value See Also Examples

Description

Function for converting the information stored in the clusterLegend slot into other useful formats.

Most of these functions are called internally by plotting functions, but are exported in case the user finds them useful.

Usage

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makeBlankData(data, groupsOfFeatures, nBlankLines = 1)

## S4 method for signature 'ClusterExperiment'
convertClusterLegend(object,
  output = c("plotAndLegend", "aheatmapFormat", "matrixNames",
  "matrixColors"))

showBigPalette(wh = NULL)

setBreaks(data, breaks = NA, makeSymmetric = FALSE)

bigPalette

showHeatmapPalettes()

seqPal5

seqPal2

seqPal3

seqPal4

seqPal1

Arguments

data

matrix with samples on columns and features on rows.

groupsOfFeatures

list, with each element of the list containing a vector of numeric indices.

nBlankLines

the number of blank lines to add in the data matrix to separate the groups of indices (will govern the amount of white space if data is then fed to heatmap.)

object

a ClusterExperiment object.

output

character value, indicating desired type of conversion.

wh

numeric. Which colors to plot. Must be a numeric vector with values between 1 and 62.

breaks

either vector of breaks, or number of breaks (integer) or a number between 0 and 1 indicating a quantile, between which evenly spaced breaks should be calculated.

makeSymmetric

whether to make the range of the breaks symmetric around zero (only used if not all of the data is non-positive and not all of the data is non-negative)

Format

An object of class character of length 60.

Details

makeBlankData pulls the data corresponding to the row indices in groupsOfFeatures adds lines of NA values into data between these groups. When given to heatmap, will create white space between these groups of features.

convertClusterLegend pulls out information stored in the clusterLegend slot of the object and returns it in useful format.

bigPalette is a long palette of colors (length 62) used by plotClusters and accompanying functions. showBigPalette creates plot that gives index of each color in bigPalette.

showBigPalette will plot the bigPalette functions with their labels and index.

setBreaks gives a set of breaks (of length 52) equally spaced between the boundaries of the data. If breaks is between 0 and 1, then the evenly spaced breaks are between these quantiles of the data.

seqPal1-seqPal4 are palettes for the heatmap. showHeatmapPalettes will show you these palettes.

Value

makeBlankData returns a list with items

If output="plotAndLegend", "convertClusterLegend" will return a list that provides the necessary information to color samples according to cluster and create a legend for it:

If output="aheatmap" a conversion of the clusterLegend to be in the format requested by aheatmap. The column 'name' is used for the names and the column 'color' for the color of the clusters.

If output="matrixNames" or "matrixColors" a matrix the same dimension of clusterMatrix(object), but with the cluster color or cluster name instead of the clusterIds, respectively.

See Also

plotHeatmap

Examples

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data(simData)

x <- makeBlankData(simData[,1:10], groupsOfFeatures=list(c(5, 2, 3), c(20,
34, 25)))
plotHeatmap(x$dataWBlanks,clusterFeatures=FALSE)
showBigPalette()
setBreaks(data=simData,breaks=.9)

#show the palette colors
showHeatmapPalettes()

#compare the palettes on heatmap
cl <- clusterSingle(simData, subsample=FALSE,
sequential=FALSE, mainClusterArgs=list(clusterFunction="pam", clusterArgs=list(k=8)))

## Not run: 
par(mfrow=c(2,3))
plotHeatmap(cl, colorScale=seqPal1, main="seqPal1")
plotHeatmap(cl, colorScale=seqPal2, main="seqPal2")
plotHeatmap(cl, colorScale=seqPal3, main="seqPal3")
plotHeatmap(cl, colorScale=seqPal4, main="seqPal4")
plotHeatmap(cl, colorScale=seqPal5, main="seqPal5")
par(mfrow=c(1,1))

## End(Not run)

clusterExperiment documentation built on Nov. 17, 2017, 8:35 a.m.