generate_plots: Generate plots of genome, chromosomes and zones.

In zh9118/GenomicOZone: Delineate outstanding genomic zones of differential gene activity

Description

Generate the plot from the processed GenomicOZone dataset object, including genome plots, chromosome plots and zone plots.

Usage

plot_genome(GOZ.ds, plot.file,
            alpha = 0.05, min.effect.size = 0.8,
            plot.width = NULL, plot.height = NULL)

plot_chromosomes(GOZ.ds, plot.file,
            alpha = 0.05, min.effect.size = 0.8,
            plot.width = NULL, plot.height = NULL)

plot_zones(GOZ.ds, plot.file,
            alpha = 0.05, min.effect.size = 0.8,
            log.exp = TRUE, plot.all.zones = FALSE)

Arguments

GOZ.ds	a GenomicOZong dataset object after running GenomicOZone function.
plot.file	a output file name. The file type is "pdf".
alpha	a cutoff for selecting adjuted p-values.
min.effect.size	the minimum effect size required for an outstanding zone. The effect size for ANOVA ranging from 0 to 1 is calculated by R package sjstats \insertCitesjstats2019GenomicOZone. Default to 0.8.
plot.width	a numerical number to specify the width of page in the plot. Using NULL will automatically determine the page width. Default is NULL.
plot.height	a numerical number to specify the height of page in the plot. Using NULL will automatically determine the page height. Default is NULL.
log.exp	a logical indicating whether to use log-scaled activity in the plot.
plot.all.zones	a logical indicating whether to plot all zones into the file. If FALSE, only outstanding genomic zones will be plotted.

Details

The three functions plot visualizations of the genome, chromosomes and zones. The R packages ggplot2 \insertCiteWickham2016ggplot2GenomicOZone and ggbio \insertCiteyin2012ggbioGenomicOZone are used to generate the plots.

The function plot_genome plots the genome-wide overviews with marked significant differential zones.

The function plot_chromosomes plots the chromosome-wide heatmap of normalized and linearized activity between sorted zones and samples, visualizing the zones with significant ones marked.

The function plot_zones plots the line chart and box-plot of the activity of the genes within each significant zone, visualizing gene activity changes over sample conditions.

Value

The function takes an input of a object, which has been created by GOZDataSet and and processed by GenomicOZone. The functions accesse the object and generate visualizations. See GOZDataSet for how to create the input object. See GenomicOZone for how to process the input object and perform the analysis.

References

\insertAllCited

Examples

  # Create an example of GOZ.ds
  data <- matrix(c(1,5,2,6,5,1,6,2), ncol = 2, byrow = TRUE)
  rownames(data) <- paste("Gene", 1:4, sep='')
  colnames(data) <- paste("Sample", c(1:2), sep='')

  colData <- data.frame(Sample_name = paste("Sample", c(1:2), sep=''),
                        Condition = c("Cancer", "Normal"))

  design <- ~ Condition

  rowData.GRanges <- GRanges(seqnames = Rle(rep("chr1", 4)),
                             ranges = IRanges(start = c(1,2,3,4), end = c(5,6,7,8)))
  names(rowData.GRanges) <- paste("Gene", 1:4, sep='')

  ks <- c(2)
  names(ks) <- "chr1"

  GOZ.ds <- GOZDataSet(data, colData, design,
                       rowData.GRanges = rowData.GRanges,
                       ks = ks)
  ####

  # Run the zoing process
  GOZ.ds <- GenomicOZone(GOZ.ds)
  ####

  # Generate plots
  plot_genome(GOZ.ds, plot.file = "Test_genome.pdf",
              plot.width = 15, plot.height = 4)

  plot_chromosomes(GOZ.ds, plot.file = "Test_chromosome.pdf",
                   plot.width = 20, plot.height = 4)

  plot_zones(GOZ.ds, plot.file = "Test_zone.pdf",
             plot.all.zones = FALSE)

zh9118/GenomicOZone documentation built on March 11, 2021, 8:11 p.m.