plotHeatmap: Plot structured z-value heatmaps of differentially expressed...

In YosefLab/ImpulseDE2: Differential expression analysis of longitudinal count data sets

Plot structured z-value heatmaps of differentially expressed genes

Description

Creates a complexHeatmap heatmap structured into subsets of genes according to their behaviour and sorted by peak time for raw counts and for the fitted signal.

Usage

plotHeatmap(objectImpulseDE2, strCondition, boolIdentifyTransients,
  scaQThres = 0.01)

Arguments

objectImpulseDE2	(instance of class ImpulseDE2Object) ImpulseDE2 output object to create heatmap from.
strCondition	(str) 'case','control','combined Heatmap is created from samples of this condition.
boolIdentifyTransients	(bool) Whether to structure heatmap into transient and transition trajectories, only possible if sigmoids were fit to the indicated condition.
scaQThres	(scalar) FDR-corrected p-value threshold for calling differentially expressed genes: Only genes below this threshold are included in the heatmap.

Value

(list length 3)

• complexHeatmapRaw (complexHeatmap plot) Heatmap of raw data by time point: Average of the size factor (and batch factor) normalised counts per time point and gene. Plot with draw(complexHeatmapRaw).

• complexHeatmapFit (complexHeatmap plot) Heatmap of impulse-fitted data by time point. Plot with draw(complexHeatmapFit).

• lsvecGeneGroups (list) List of gene ID vectors: One per heatmap group with all gene IDs of the the profiles displayed in the heatmap.

Author(s)

David Sebastian Fischer

See Also

Called seperately by used.

Examples

library(ComplexHeatmap)
lsSimulatedData <- simulateDataSetImpulseDE2(
vecTimePointsA   = rep(seq(1,8),3),
vecTimePointsB   = NULL,
vecBatchesA      = NULL,
vecBatchesB      = NULL,
scaNConst        = 0,
scaNImp          = 50,
scaNLin          = 0,
scaNSig          = 50)
objectImpulseDE2 <- runImpulseDE2(
matCountData    = lsSimulatedData$matObservedCounts, 
dfAnnotation    = lsSimulatedData$dfAnnotation,
boolCaseCtrl    = FALSE,
vecConfounders  = NULL,
boolIdentifyTransients = TRUE,
scaNProc        = 1 )
lsHeatmaps <- plotHeatmap(
objectImpulseDE2=objectImpulseDE2,
strCondition='case',
boolIdentifyTransients=TRUE,
scaQThres=0.01)
draw(lsHeatmaps$complexHeatmapRaw)

YosefLab/ImpulseDE2 documentation built on Sept. 17, 2022, 2:45 a.m.