plotting: chromstaR plotting functions

In chromstaR: Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

Description

This page provides an overview of all chromstaR plotting functions.

Details

Plotting functions that work on uniHMM objects:

plotHistogram

Read count histogram with fitted mixture distributions.

Plotting functions that work on multiHMM objects:

heatmapCountCorrelation

Heatmap of read count correlations.

heatmapTransitionProbs

Heatmap of transition probabilities of the Hidden Markov Model.

heatmapCombinations

Binary presence/absence pattern of combinatorial states.

plotExpression

Boxplot of expression values that overlap combinatorial states.

Plotting functions that work on multiHMM and combinedMultiHMM objects:

heatmapCountCorrelation

Heatmap of read count correlations.

plotEnrichCountHeatmap

Heatmap of read counts around annotation.

plotEnrichment

Enrichment of combinatorial states around annotation.

plotFoldEnrichHeatmap

Enrichment of combinatorial states at multiple annotations.

plotExpression

Boxplot of expression values that overlap combinatorial states.

Other plotting functions:

heatmapCombinations

Binary presence/absence pattern of combinatorial states.

chromstaR documentation built on Nov. 8, 2020, 8:29 p.m.