multi_profile_plots: 'EnrichedHeatmap' plots and 'ComplexHeatmaps' for multiple...
In lakhanp1/chipmine: Analyze ChIP-seq Data

Description Usage Arguments Value Examples

View source: R/p06_profile_plot_list_functions.R

This method generates profile heatmaps for multiple samples. Optionally, if the sample list has any polII samples, it also generate a heatmap for the polII expression values.

multi_profile_plots(
  exptInfo,
  genesToPlot,
  clusters = NULL,
  drawClusterAn = TRUE,
  clusterColor = NULL,
  clustOrd = NULL,
  profileColors = NULL,
  matSource = "normalizedmatrix",
  targetType = "region",
  targetName = "gene",
  matBins = c(200, 200, 100, 10),
  ylimFraction = NULL,
  plotExpression = FALSE,
  expressionData = NULL,
  expressionColor = NULL,
  keep = c(0, 1),
  rasterize = TRUE,
  rasterQual = 5,
  ...
)

`exptInfo`	experiment info as data frame with information like sampleID, type, path etc
`genesToPlot`	A vector of gene IDs which are to be plotted
`clusters`	Dataframe with cluster information. Two columns must be present in this dataframe: 'cluster', 'geneId'. Default: NULL
`drawClusterAn`	Logical: Whether to add row annotation heatmap to heatmap list. Default: TRUE
`clusterColor`	cluster annotation color information. Default: NULL
`clustOrd`	A character vector of cluster order in the plot. If not provided, clusters are arranged as per character sort order
`profileColors`	a named list of color objects for each of the sample. Color for profile heatmap should be generated by colorRamp2
`matSource`	Method by which profile matrix was generated. One of deeptools, miao, normalizedmatrix. Default: normalizedmatrix
`targetType`	One of "region", "point". If targetType is "region", target is used to decide the number of bins over region. Otherwise, for "point", a signle point matrix is expected where the region is extracted around single point. Default: region
`targetName`	Name to be used for target. Eg: "gene", "TSS", "TES", "summit" etc. default: gene
`matBins`	A vector with four elements representing the column counts for up, body, down regions and binSize for the profile matrix. Default: `c(200, 200, 100, 10)`
`ylimFraction`	A named list with intensity scores to use as ylimit for top annotation. If the value is single number, it has to be floating point number to extract the quantile and use limit `[0, quantile(x)]`. If the value is numeric vector of length 2, the two numbers are used as lower and upper limits for ylimit of top annotation. Default: NULL.
`plotExpression`	Binry: whether to plot polII expression heatmap or not. Default: FALSE
`expressionData`	an dataframe which has info: clustering, polII expression, TF binding status for each gene etc. Default: NULL
`expressionColor`	color object for polII expression heatmap
`keep`	Same as `EnrichedHeatmap::normalizeToMatrix`. First value is used as lower quantile and any value in profile matrix less than lower quantile is set to lower quantile. Second value is used as upper quantile and any value greater than upper quantile is set to upper quantile. Default: `c(0, 1)`
`rasterize`	Binary: whether to rasterize the profile heatmap or not. By default this is set as TRUE for multiple profile plots.
`rasterQual`	Raster quality. This is the `raster_quality` argument `Heatmap` function. in Default: 5
`...`	Other arguments for EnrichedHeatmap function

A list object with following elements:

heatmapList: a heatmap list object which has profile heatmaps and optionally expression heatmaps
profileHeatmaps: a named list of profile heatmaps generated by EnrichedHeatmap
expressionHeatmaps: a named list of polII signal heatmaps
plotGaps: a vector with required gaps between heatmaps while generating multiprofile plots
profileColors: a named list object with color scale used for each profile heatmap
expressionColor: a named list object with color scale used for each expression heatmap