profile_heatmap: Generate profile heatmap
In lakhanp1/chipmine: Analyze ChIP-seq Data

Description Usage Arguments Value Examples

This function generate a profile heatmap using EnrichedHeatmap function. The genes are clustered into different groups based on the profile using k-means clustering algorithm. Optionally, the prior clustering information can be provided through argument geneGroups

profile_heatmap(
  profileMat,
  signalName,
  profileColor,
  columnTitle = NULL,
  createClusters = FALSE,
  numClust = 7,
  geneGroups = NULL,
  showAnnotation = TRUE,
  clusterColor = NULL,
  ylimFraction = NULL,
  posLineGpar = gpar(lty = 2, alpha = 0.4, lwd = 0.5),
  rasterPar = list(use = TRUE, qual = 5),
  ...
)

`profileMat`	profile matrix of class `normalizedMatrix`
`signalName`	name of the signal track
`profileColor`	Color function for profile heatmap generated by `colorRamp2`
`columnTitle`	title to be placed on the column. Default: signalName
`createClusters`	Logical: whether or not to do kmeans clustering. If FALSE, clusterStorePath must be provided which has the cluster data. Default: FALSE
`numClust`	number of clusters to generate using k-means clustering. Default: 7
`geneGroups`	Either a dataframe or a file path with cluster information or NULL. Two columns must be present in this dataframe: `geneId, cluster`. In case it is NULL, heatmap rows are not split into different groups.
`showAnnotation`	Logical: to show or hide top annotation. Default: TRUE
`clusterColor`	Color assignment object for cluster colors. If nothing provided, colors are generated internally. Default: NULL
`ylimFraction`	A numeric vector with one or two elements for deciding the `ylimit` of top profile heatmap 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.
`posLineGpar`	`pos_line_gp` parameter of `EnrichedHeatmap`. Default: `gpar(lty = 2, alpha = 0.4, lwd = 0.5)`
`rasterPar`	rasterization parameters as list() with two elements: use, qual. Default: `list(use = TRUE, qual = 5)`. `rasterPar$use` is used for `use_raster` argument and `rasterPar$qual` is used for `raster_quality` argument of `Heatmap` function.
`...`	Other arguments for EnrichedHeatmap function