MultiRepMacsChIPSeq - plot_peak_figures

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plot_peak_figures.R

This script generates a number of heat maps and plots for identified peak calls, including the following:

• Stacked bar chart of unique and duplicate fragment counts
• Scatter plot of before and after duplication counts versus non-duplicate
• PCA plot between all sample replicates based on fragment counts in peak
• Multiple pairwise correlation (Pearson, Spearman, and Euclidean distance) heat maps and clusters of the counts between sample replicates
• Bar chart plots for peak number and genomic space for each sample peaks
• Box and whisker plots for peak length distributions
• Line plot for ranked peak signals for each sample replicate
• Heat map and cluster of the number of peak intersections
• Heat map and cluster of jaccard (spatial overlap) statistic between peaks
• Pie chart of spatial overlap fraction of total merged peak coverage for each sample
• UpSet plot of peak interactions
• UpSet plot of peak spatial overlaps (optional, compute intensive)
• Bar chart of the fraction of fragment counts in corresponding peaks for each replicate, a measure of ChIP efficiency
• Heat map of the mean q-value scores for each ChIP over merged peaks
• Heat map of the mean log2 fold enrichment for each ChIP over merged peaks with k-means clustering (4, 6, and 8 clusters)
• Profile heat map of the fragment density over the midpoint of merged peaks for all samples, with and without k-means (4) clustering, or clustered by sample calls
• Profile heat map of the log2 Fold Enrichment over the midpoint of merged peaks for all samples, with and without k-means (4) clustering, or clustered by sample calls
• Mean profile line plot of fragment density over merged peaks, including for each group sample calls
• Mean profile line plot of log2 Fold Enrichment over merged peaks, including for each group of sample calls

Samples are identified by color palette: Try Set1, Set2, Set3, Spectral, Dark2, or any other named palette in RColorBrewer. Note that excessive sample numbers may exceed the number the colors in a given palette (8 to 12).

USAGE:

plot_peak_figures.R [options]

OPTIONS:

-i INPUT, --input=INPUT
	Path and basename to the multirep_macs2_pipeline combined output

-n MIN, --min=MIN
	Minimum log2 Fold Enrichment value to plot, default -4

-x MAX, --max=MAX
	Maximum log2 Fold Enrichment value to plot, default 4

-q QMAX, --qmax=QMAX
	Maximum q-value to plot, default 30

-r FMAX, --fmax=FMAX
	Maximum fragment value to plot, default 4

--mincluster=MINCLUSTER
	Minimum number of peaks to generate k-means plots, default 500

--spatial
        Generate spatial UpSet plots (compute intensive), default F

-p PALETTE --palette=PALETTE
	RColorBrewer palette for samples, default Set1

-f FORMAT, --format=FORMAT
	Format of output file: png, pdf, default png

-h, --help
	Show this help message and exit