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

View source: R/lolaUtils.R

lolaRegionSetHeatmapR Documentation

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 Sept. 8, 2023, 4:32 p.m.