lolaRegionSetHeatmap: lolaRegionSetHeatmap Plot a heatmap in which the rows are...

In demuellae/muRtools: Mueller's R tools

lolaRegionSetHeatmap Plot a heatmap in which the rows are different user sets and the color corresponds to an enrichment score

Description

lolaRegionSetHeatmap Plot a heatmap in which the rows are different user sets and the color corresponds to an enrichment score

Usage

lolaRegionSetHeatmap(
  lolaDb,
  lolaRes,
  scoreCol = "pValueLog",
  orderCol = scoreCol,
  signifCol = "qValue",
  markSignif = FALSE,
  includedCollections = c(),
  recalc = TRUE,
  pvalCut = 0.01,
  maxTerms = 50,
  userSetOrder = NULL,
  colorpanel = colpal.cont(9, "cb.OrRd"),
  colorpanelLimits = rep(as.numeric(NA), 2),
  groupByCollection = TRUE,
  orderDecreasing = NULL,
  appendTermDbId = TRUE
)

Arguments

lolaDb	LOLA DB object as returned by LOLA::loadRegionDB or loadLolaDbs
lolaRes	LOLA enrichment result as returned by the runLOLA function from the LOLA package
scoreCol	column name in lolaRes to be plotted
orderCol	column name in lolaRes which is used for sorting the results
signifCol	column name of the significance score in lolaRes. Should be one of c("pValueLog", "qValue")
markSignif	mark significant enrichments in the heatmap
includedCollections	vector of collection names to be included in the plot. If empty (default), all collections are used
recalc	recalculate adjusted p-value/q-value and ranks after the specified subsetting (by includedCollections)
pvalCut	p-value cutoff (negative log10) to be employed for filtering the results
maxTerms	maximum number of items to be included in the plot
userSetOrder	the order in which the user sets are displayed. NULL (default) means original factor levels if userSet is a factor or (alphanumeric) sorting otherwise; "nSignif" means in decreasing order of significant terms; "clusterSignif" means hierarchical clustering by occurrences of significant terms;
colorpanel	colorpanel for the heatmap gradient
groupByCollection	facet the plot by collection
orderDecreasing	flag indicating whether the value in orderCol should be considered as decreasing (as opposed to increasing). NULL (default) for automatic determination.
appendTermDbId	attach the index of the item in the LOLA DB object to the name of the set

Value

ggplot object containing the plot

Author(s)

Fabian Mueller

demuellae/muRtools documentation built on Nov. 6, 2024, 9:44 a.m.