plotHeatmap {seqplots} | R Documentation

## Plot heatmap with optional clustering

### Description

Draw the heatmap plot from `PlotSetArray`, `PlotSetList`, `PlotSetPair` classes or properly formatted `list` (see details) in active graphics window. Axes and titles, keys and other plot elements are controlled by function parameters.

### Usage

    plotHeatmap(plotset, main = "", labels = NA, legend = TRUE,
      keepratio = FALSE, plotScale = "no", sortrows = FALSE,
      clusters = 5L, clstmethod = "kmeans", include = NULL,
      ssomt1 = 2L, ssomt2 = 2L, cex.main = 16, cex.lab = 12,
      cex.axis = 12, cex.legend = 12, xlab = "", ylab = "",
      autoscale = TRUE, zmin = 0, zmax = 10, xlim = NULL,
      ln.v = TRUE, s = 0.01, indi = TRUE, o_min = NA, o_max = NA,
      colvec = NULL, clspace = NULL, pointsize = 12, embed = FALSE,
      ggplot = FALSE, raster = FALSE, plotz = TRUE, FO = NULL,
      CL = NA, sort_by = NULL, sort_mids = FALSE, sort_dst = 0L,
      clst_mids = FALSE, ...)

    ## S4 method for signature 'list'
    plotHeatmap(plotset, main = "", labels = NA,
      legend = TRUE, keepratio = FALSE, plotScale = "no",
      sortrows = FALSE, clusters = 5L, clstmethod = "kmeans",
      include = NULL, ssomt1 = 2L, ssomt2 = 2L, cex.main = 16,
      cex.lab = 12, cex.axis = 12, cex.legend = 12, xlab = "",
      ylab = "", autoscale = TRUE, zmin = 0, zmax = 10, xlim = NULL,
      ln.v = TRUE, s = 0.01, indi = TRUE, o_min = NA, o_max = NA,
      colvec = NULL, clspace = NULL, pointsize = 12, embed = FALSE,
      ggplot = FALSE, raster = FALSE, plotz = TRUE, FO = NULL,
      CL = NA, sort_by = NULL, sort_mids = FALSE, sort_dst = 0L,
      clst_mids = FALSE, ...)

    ## S4 method for signature 'PlotSetPair'
    plotHeatmap(plotset, main = "", labels = NA,
      legend = TRUE, keepratio = FALSE, plotScale = "no",
      sortrows = FALSE, clusters = 5L, clstmethod = "kmeans",
      include = NULL, ssomt1 = 2L, ssomt2 = 2L, cex.main = 16,
      cex.lab = 12, cex.axis = 12, cex.legend = 12, xlab = "",
      ylab = "", autoscale = TRUE, zmin = 0, zmax = 10, xlim = NULL,
      ln.v = TRUE, s = 0.01, indi = TRUE, o_min = NA, o_max = NA,
      colvec = NULL, clspace = NULL, pointsize = 12, embed = FALSE,
      ggplot = FALSE, raster = FALSE, plotz = TRUE, FO = NULL,
      CL = NA, sort_by = NULL, sort_mids = FALSE, sort_dst = 0L,
      clst_mids = FALSE, ...)

    ## S4 method for signature 'PlotSetList'
    plotHeatmap(plotset, main = "", labels = NA,
      legend = TRUE, keepratio = FALSE, plotScale = "no",
      sortrows = FALSE, clusters = 5L, clstmethod = "kmeans",
      include = NULL, ssomt1 = 2L, ssomt2 = 2L, cex.main = 16,
      cex.lab = 12, cex.axis = 12, cex.legend = 12, xlab = "",
      ylab = "", autoscale = TRUE, zmin = 0, zmax = 10, xlim = NULL,
      ln.v = TRUE, s = 0.01, indi = TRUE, o_min = NA, o_max = NA,
      colvec = NULL, clspace = NULL, pointsize = 12, embed = FALSE,
      ggplot = FALSE, raster = FALSE, plotz = TRUE, FO = NULL,
      CL = NA, sort_by = NULL, sort_mids = FALSE, sort_dst = 0L,
      clst_mids = FALSE, ...)

    ## S4 method for signature 'PlotSetArray'
    plotHeatmap(plotset, main = "", labels = NA,
      legend = TRUE, keepratio = FALSE, plotScale = "no",
      sortrows = FALSE, clusters = 5L, clstmethod = "kmeans",
      include = NULL, ssomt1 = 2L, ssomt2 = 2L, cex.main = 16,
      cex.lab = 12, cex.axis = 12, cex.legend = 12, xlab = "",
      ylab = "", autoscale = TRUE, zmin = 0, zmax = 10, xlim = NULL,
      ln.v = TRUE, s = 0.01, indi = TRUE, o_min = NA, o_max = NA,
      colvec = NULL, clspace = NULL, pointsize = 12, embed = FALSE,
      ggplot = FALSE, raster = FALSE, plotz = TRUE, FO = NULL,
      CL = NA, sort_by = NULL, sort_mids = FALSE, sort_dst = 0L,
      clst_mids = FALSE, ...)

### Arguments

`plotset` | The dataset to plot - can be `PlotSetArray`, `PlotSetList`, `PlotSetPair` or properly formatted `list`
`main` | The main title of the plot, shown in top-centre part of the figure; defaults to NULL (not visible)
`labels` | The character vector giving sub-titles of heatmaps (plotted over the heatmap and below the main title). The defaults NULL value indicates that feature/track file names will be used to generate the sub-titles.
`legend` | if TRUE plot the colour key
`keepratio` | If TRUE keep 1:1 aspect ratio of the figure; defaults to FALSE
`plotScale` | scale the available data before plotting, can be "linear" (do not scale, default), "log2" or "zscore"
`sortrows` | If `"increasing"` or `"decreasing"` the rows of heatmap will be sorted by mean value across all heatmaps, defaults to `FALSE` - not sorted. For backwards compatibility `TRUE` is synonymous to "increasing".
`clusters` | The number of cluster for "kmeans" and "hclust", ignored for "ssom", defaults to 5L
`clstmethod` | Determines the heatmap clustering algorithm "kmeans" for k-means (default, see `kmeans`), "hclust" (see `hclust`) for hierarchical clustering, "ssom" for (super) self organising map (see `supersom`) with torus topology, "bed_scores" to use scores stored in BED/GFF file as cluster indicates, and "none" of FALSE to turn off the clustering
`include` | The logical vector indicating if given subplot should influence clustering and sorting, if given element is FALSE the sub-heatmap will be still plotted, and the order of data rows will be determined by clustering/sorting other sub-heatmaps, defaults to NULL, which incluses all - equivalent to `rep(TRUE, length(plotset))`
`ssomt1` | Determines , the dimensionality of SOM - number of neurons in 1st dimension, number of resulting clusters equals ssomt1*ssomt2, defaults to 2L
`ssomt2` | Determines , the dimensionality of SOM - number of neurons in 2st dimension, number of resulting clusters equals ssomt1*ssomt2, defaults to 2L
`cex.main` | Main title font size in points, defaults to 16
`cex.lab` | Axis labels font size in points, Defaults to 12
`cex.axis` | Axis numbers font size in points, defaults to 12
`cex.legend` | Keys labels font size in points, defaults to 12
`xlab` | label below x-axis
`ylab` | label below y-axis
`autoscale` | if TRUE the colour keys will be auto scaled
`zmin` | global minimum value on colour key, ignored if `autoscale` is TRUE
`zmax` | global maximum value on colour key, ignored if `autoscale` is TRUE
`xlim` | the x limits (x1, x2) of the plot. Note that x1 > x2 is allowed and leads to a "reversed axis". The default value, NULL, indicates that the whole range present in `plotset` will be plotted.
`ln.v` | Determins if vertical guide line(s) should be plotted (TRUE) or ommitted (FALSE). For anchored plots 2 lines indicating the start and end of anchored distance are plotted.
`s` | The saturation value used to auto scale colour key limits, defaults to 0.01
`indi` | If TRUE (defaults) the independent colour keys will be plotted below heatmaps, if FALSE the commmon colour key is shown rightmost
`o_min` | vector of length equal to number of sub heatmaps determining minimum value on color key for each sub plot, if NULL (default) or NA the global settings are used, ignored in `indi` is FALSE
`o_max` | vector of length equal to number of sub heatmaps determining maximum value on color key for each sub plot, if NULL (default) or NA the global settings are used, ignored in `indi` is FALSE
`colvec` | The vector or list of colour values used generate sub-heatmaps colorspaces. If NULL (default) the automatically generated colour values will be used for all sub-heatmaps. If single color is provided, the sequential colorspace reging from given color to white will be created. If the vector of colors is provided, the continous pallete will be created using these colors. NA value indicates default color pallete to be used for give sub-heatmap. Accepted values are: vector of any of the three kinds of R colour specifications, i.e., either a color name (as listed by colors()), a hexadecimal string of the form "#rrggbb" or "#rrggbbaa" (see rgb), or a positive integer i meaning palette()[i]. See `col2rgb`.
`clspace` | The colours pace of the heatmap, see `grDevices`
`pointsize` | The default font point size to be used for plots. Defaults to 12 (1/72 inch).
`embed` | If TRUE plot single (first) heatmap without using grid system. Useful to embed heatmap in complex layouts, see `layout` and `par` for details. Defaults to FALSE.
`ggplot` | Use ggplot2 package instead of standard R graphics, defaults to FALSE
`raster` | The bitmap raster is used to plot the heatmap image, see "useRaster" option in `image` function and `geom_raster` function for details, defaults to FALSE
`plotz` | if FALSE the functions returns a list of plot parameters, rather than actual plot
`FO` | If set, this vector determines a final order of features in the heatmap
`CL` | If set, this vector determines a class assignment of features in the heatmap
`sort_by` | Set which subplots contribute to sorting
`sort_mids` | For anchored plot, sort using only middle values
`sort_dst` | For anchored plot, the flanking distance that should be added to sorting calculation
`clst_mids` | For anchored plot, cluster using only middle values
`...` | parameters passed to internal plotting function

### Value

The cluster report `data.frame`, giving cluster assignments and sorting order for each feature. It contains following columns:

- originalOrder - number of feature (row) in GFF/BED, can be used to restore original order after sorting on cluster ID

- ClusterID - the numeric ID of the cluster. The topmost cluster on the heatmap is annotated with 1, and the bottom cluster with k, where k equals to number of clusters selected, exported only if clustering is enabled

- SortingOrder - the order imposed on heatmap by sorting by mean row(s) values, exported only if sorting is enabled

- FinalOrder - the final order of heatmap's rows, this can be influenced by sorting and clustering; 1 indicates topmost row

### Methods (by class)

- `list`: Method for signature `list` with following format: `list[[FEATURE]][[TRACK/MOTIF]][[KEY_VALUE]]`

- `PlotSetPair`: Method for signature `PlotSetPair`

- `PlotSetList`: Method for signature `PlotSetList`

- `PlotSetArray`: Method for signature `PlotSetArray`

### See Also

Other plotting functions: `getPlotSetArray`, `plotAverage`, `plot`

### Examples

    # Get the paths of example files
    bed1 <- system.file("extdata",
         "Transcripts_ce10_chrI_100Kb.bed", package="seqplots")
    bed2 <- system.file("extdata",
         "GSM1208361_chrI_100Kb_PeakCalls.bed", package="seqplots")
    bw1 <- system.file("extdata",
         "GSM1208360_chrI_100Kb_q5_sample.bw", package="seqplots")

    #If required install C. elegans genomic package from Bioconductor
    if(!"BSgenome.Celegans.UCSC.ce10" %in% BSgenome::installed.genomes()) {
        if(.Platform$OS.type != "windows" || .Machine$sizeof.pointer != 4) {
             if (!requireNamespace("BiocManager", quietly=TRUE))
             install.packages("BiocManager")
             BiocManager::install("BSgenome.Celegans.UCSC.ce10")
         }
    }

    #Get getPlotSetArray for track and feature files
    if(.Platform$OS.type != "windows" || .Machine$sizeof.pointer != 4) {
        plotset1 <- getPlotSetArray(bw1, c(bed1, bed2), 'ce10')
    } else {
        load(system.file("extdata", "precalc_plotset.Rdata", package="seqplots"))
    }

    # equivalent to plot(plotset1, what='h') or plotset1$plot(what='h')
    plotHeatmap(plotset1[1])

[Package seqplots version 1.24.0 Index]