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Plot DMGs circos across chromosomes

Source: R/plot_dmg_circos.R
plot_dmg_circos.Rd

Plot genome-wide DMGs circos with separate tracks for hyper/hypo and top-gene annotations.

Usage

plot_dmg_circos(
  dmr_file,
  gff_file = NULL,
  format = "auto",
  label_type = "name",
  gene_table = NULL,
  y_transform = "none",
  chrom_height = 0.08,
  chrom_color = "#eeeeee",
  chrom_border = "#cccccc",
  chrom_cex = 0.8,
  gap_degree = 1,
  x_tick_by = 2e+07,
  axis_cex = 0.5,
  last_gap_degree = 3,
  scatter_height = 0.15,
  top_up = 30,
  top_down = 30,
  up_color = "#ff0000",
  down_color = "#008800",
  point_cex = 0.5,
  annotation_height = 0.18,
  label_cex = 0.5,
  label_rotate = 0,
  label_font = 1,
  connector_lwd = 0.5,
  connector_col = "#333333",
  connector_len = 0.2,
  connector_elbow = 0.8
)

Arguments

dmr_file

DEG table from MethylKit analysis.

gff_file

Genomic structural annotation GFF3/GTF file path.

format

Format of GFF3/GTF file. ("auto", "gff3", "gtf").

label_type

Label by gene name or gene id. ("name", "id").

gene_table

Optional gene ID/name mapping table (first two columns: id, name).

y_transform

Y-axis transformation for meth.diff. ("none", "log2", "log10").

chrom_height

Chrom track height. (0.08).

chrom_color

Chromosome track fill color. ("#eeeeee").

chrom_border

Chromosome track border color. ("#333333").

chrom_cex

Chrom name cex. (0.8).

gap_degree

Gap degree between chromosomes. (1).

x_tick_by

Chromosome axis tick step (bp). (2e7).

axis_cex

Axis text cex. (0.5).

last_gap_degree

Gap degree between last and first chromosome. (3).

scatter_height

Scatter track height. (0.15).

top_up

Number of top hyper-methylated DMGs to annotate. (30).

top_down

Number of top hypo-methylated DMGs to annotate. (30).

up_color

Point color for hyper-methylated DMGs. ("#ff0000").

down_color

Point color for hypo-methylated DMGs. ("#008800").

point_cex

Point size (cex). (0.5).

annotation_height

Track height for annotation rings. (0.15).

label_cex

Label size (cex) for top-gene annotations. (0.5).

label_rotate

Label rotation degree (counterclockwise). (0).

label_font

Font for chromosome and gene labels. (1).

connector_lwd

Line width for point-label connectors. (0.5).

connector_col

Color for point-label connectors. ("#333333").

connector_len

Connector length. (0.2).

connector_elbow

Connector elbow. (0.8).

Value

Plot of DMGs circos across chromosomes.

Author

benben-miao

Examples

dmr_file <- system.file(
  "extdata",
  "example.dmr",
  package = "GAnnoViz")

gff_file <- system.file(
  "extdata",
  "example.gff3.gz",
  package = "GAnnoViz")

plot_dmg_circos(
  dmr_file = dmr_file,
  gff_file = gff_file,
  format = "auto",
  label_type = "name",
  gene_table = NULL,
  y_transform = "none",
  chrom_height = 0.08,
  chrom_color = "#eeeeee",
  chrom_border = "#cccccc",
  chrom_cex = 0.8,
  gap_degree = 1,
  x_tick_by = 2e7,
  axis_cex = 0.5,
  last_gap_degree = 3,
  scatter_height = 0.15,
  top_up = 30,
  top_down = 30,
  up_color = "#ff0000",
  down_color = "#008800",
  point_cex = 0.5,
  annotation_height = 0.18,
  label_cex = 0.5,
  label_rotate = 0,
  label_font = 1,
  connector_lwd = 0.5,
  connector_col = "#333333",
  connector_len = 0.2,
  connector_elbow = 0.8
)
#> Import genomic features from the file as a GRanges object ... 
#> OK
#> Prepare the 'metadata' data frame ... 
#> OK
#> Make the TxDb object ... 
#> OK