seqplots (version 1.10.2)

plotHeatmap: 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, ...)
## S3 method for class '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, ...)
## S3 method for class '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, ...)
## S3 method for class '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, ...)
## S3 method for class '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, ...)

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 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

...

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 signaturelistwith following format:list[[FEATURE]][[TRACK/MOTIF]][[KEY_VALUE]]
• PlotSetPair: Method for signaturePlotSetPair
• PlotSetList: Method for signaturePlotSetList
• PlotSetArray: Method for signaturePlotSetArray

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) {
         source("http://bioconductor.org/biocLite.R")
         biocLite("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])