plotClustersTable: Plot heatmap of cross-tabs of 2 clusterings
In clusterExperiment: Compare Clusterings for Single-Cell Sequencing

Description Usage Arguments Details Value Author(s) See Also Examples

Plot heatmap of cross-tabulations of two clusterings

## S4 method for signature 'ClusterExperiment'
plotClustersTable(
  object,
  whichClusters,
  ignoreUnassigned = FALSE,
  margin = NA,
  ...
)

## S4 method for signature 'table'
plotClustersTable(
  object,
  plotType = c("heatmap", "bubble"),
  main = "",
  xlab = NULL,
  ylab = NULL,
  legend = TRUE,
  cluster = FALSE,
  clusterLegend = NULL,
  sizeTable = NULL,
  ...
)

## S4 method for signature 'ClusterExperiment'
tableClusters(
  object,
  whichClusters = "primary",
  useNames = TRUE,
  tableMethod = c("intersect", "union"),
  ...
)

## S4 method for signature 'table,table'
bubblePlot(
  propTable,
  sizeTable,
  gridColor = rgb(0, 0, 0, 0.05),
  maxCex = 8,
  cexFactor,
  ylab,
  xlab,
  propLabel = "Value of %",
  legend = TRUE,
  las = 2,
  colorScale = RColorBrewer::brewer.pal(11, "Spectral")[-6]
)

`object`	ClusterExperiment object (or matrix with table result)
`whichClusters`	argument that can be either numeric or character vector indicating the clusterings to be used. See details of `getClusterIndex`.
`ignoreUnassigned`	logical as to whether to ignore unassigned clusters in the plotting. This means they will also be ignored in the calculations of the proportions (if `margin` not NA).
`margin`	if NA, the actual counts from `tableClusters` will be plotted. Otherwise, `prop.table` will be called and the argument `margin` will be passed to `prop.table` to determine whether proportions should be calculated. If '1', then the proportions in the rows sum to 1, if '2' the proportions in the columns sum to 1. If 'NULL' then the proportion across the entire matrix will sum to 1. An additional option has been added so that if you set `margin=0`, the entry displayed in each cell will be the proportion equal to the size of the intersection over the size of the union of the clusters (a Jaccard similarity between the clusters), in which case each entry is a value between 0 and 1 but no combination of the entries sum to 1.
`...`	arguments passed on to `plotHeatmap` or `bubblePlot` depending on choice of `plotType`. Note that these functions take different arguments so that switching from one to the other may not take all arguments. In particular `bubblePlot` calls `plot` while `plotHeatmap` calls `NMF{aheatmap}`.
`plotType`	type of plot. If "heatmap", then a heatmap will be created of the values of the contingency table of the two clusters (calculated as determined by the argument "margin") using `plotHeatmap`. If "bubble", then a plot will be created using `bubblePlot`, which will create circles for each cell of the contingencey table whose size corresponds to the number of samples shared and the color based on the value of the proportion (as chosen by the argument `margin`).
`main`	title of plot, passed to `plotHeatmap` or to the argument `propLabel` in `bubblePlot`
`xlab`	label for labeling clustering on the x-axis. If NULL, will determine names. If set to `NA` no label for clustering on the x-axis will be plotted (to turn off legend of the clusterings in heatmap, set `legend=FALSE`).
`ylab`	label for labeling clustering on the y-axis. If NULL, will determine names. If set to `NA` no label for clustering on the y-axis will be plotted (to turn off legend of the clusterings in heatmap, set `legend=FALSE`).
`legend`	whether to draw legend along top (bubble plot) or the color legend (heatmap)
`cluster`	logical, whether to cluster the rows and columns of the table. Passed to arguments `clusterFeatures` AND `clusterSamples` of `plotHeatmap`.
`clusterLegend`	list in `clusterLegend` format that gives colors for the clusters tabulated.
`sizeTable`	table of sizes (only for use in `bubblePlot` or `plotType="bubble"`). See details.
`useNames`	for `tableClusters`, whether the output should be tabled with names (`useNames=TRUE`) or ids (`useNames=FALSE`)
`tableMethod`	the type of table calculation to perform. "intersect" refers to the standard contingency table (`table`), where each entry of the resulting table is the number of objects in both clusters. "union" instead gives for each entry the number of objects that are in the union of both clusters.
`propTable`	table of proportions (`bubblePlot`))
`gridColor`	color for grid lines (`bubblePlot`))
`maxCex`	largest value of cex for any point (others will scale proportionally smaller) (`bubblePlot`)).
`cexFactor`	factor to multiple by to get values of circles. If missing, finds value automatically, namely by using the maxCex value default. Overrides value of maxCex. (`bubblePlot`))
`propLabel`	the label to go with the legend of the color of the bubbles/circles
`las`	the value for the las value in the call to `axis` in labeling the clusters in the bubble plot. Determines whether parallel or perpindicular labels to the axis (see `par`).
`colorScale`	the color scale for the values of the proportion table

For plotClustersTable applied to the class table, sizeTable is passed to bubblePlot to indicate the size of the circle. If sizeTable=NULL, then it is assumed that the object argument is the table of counts and both the propTable and sizeTable are set to the same value (hence turning off the coloring of the circle/bubbles). This is equivalent effect to the margin=NA option of plotClustersTable applied to the ClusterExperiment class.

Note that the cluster labels in plotClustersTable and tableClusters are converted to "proper" R names via make.names. This is because tableClusters calls the R function table, which makes this conversion

For plotClustersTable, whichClusters should define 2 clusters, while for tableClusters it can indicate arbitrary number.

bubblePlot is mainly used internally by plotClustersTable but is made public for users who want more control and to allow documentation of the arguments. bubblePlot plots a circle for each intersection of two clusters, where the color of the circle is based on the value in propTable and the size of the circle is based on the value in sizeTable. If propTable is equal to sizeTable, then the propTable is ignored and the coloring of the circles is not performed, only the adjusting of the size of the circles based on the total size. The size is determined by setting the cex value of the point as $sqrt(sizeTable[i,j])/sqrt(max(sizeTable))*cexFactor$.

tableClusters returns an object of class table (see table).

plotClustersTables returns invisibly the plotted proportion table. In particular, this is the result of applying prop.table to the results of tableClusters (after removing unclustered samples if ignoreUnassigned=TRUE).

Kelly Street, Elizabeth Purdom

plotHeatmap

table

prop.table

#clustering using pam: try using different dimensions of pca and different k
data(simData)

cl <- clusterMany(simData, nReducedDims=c(5, 10, 50), reducedDim="PCA",
clusterFunction="pam", ks=2:4, findBestK=c(TRUE,FALSE),
removeSil=c(TRUE,FALSE), makeMissingDiss=TRUE)
#give arbitrary names to clusters for demonstration
cl<-renameClusters(cl,value=letters[1:nClusters(cl)[1]],whichCluster=1)
tableClusters(cl,whichClusters=1:2)
#show options of margin in heatmap format:
par(mfrow=c(2,3))
plotClustersTable(cl,whichClusters=1:2, margin=NA, legend=FALSE,
  ignoreUnassigned=TRUE)
plotClustersTable(cl,whichClusters=1:2, margin=0, legend=FALSE,
  ignoreUnassigned=TRUE)
plotClustersTable(cl,whichClusters=1:2, margin=1, legend=FALSE,
  ignoreUnassigned=TRUE)
plotClustersTable(cl,whichClusters=1:2, margin=2, legend=FALSE,
  ignoreUnassigned=TRUE)
plotClustersTable(cl,whichClusters=1:2, margin=NULL, legend=FALSE,
  ignoreUnassigned=TRUE)

#show options of margin in bubble format:
par(mfrow=c(2,3))
plotClustersTable(cl,whichClusters=1:2, margin=NA, 
   ignoreUnassigned=TRUE, plotType="bubble")
plotClustersTable(cl,whichClusters=1:2, margin=0,
   ignoreUnassigned=TRUE, plotType="bubble")
plotClustersTable(cl,whichClusters=1:2, margin=1,
   ignoreUnassigned=TRUE, plotType="bubble")
plotClustersTable(cl,whichClusters=1:2, margin=2,
   ignoreUnassigned=TRUE, plotType="bubble")
plotClustersTable(cl,whichClusters=1:2, margin=NULL,
   ignoreUnassigned=TRUE, plotType="bubble")