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Plot DMGs manhattan plot across chromosomes

Source: R/plot_dmg_manhattan.R
plot_dmg_manhattan.Rd

Plot genome-wide DMGs manhattan.

Usage

plot_dmg_manhattan(
  dmr_file,
  gff_file,
  format = "auto",
  gene_table = NULL,
  label_type = "name",
  label_col = NULL,
  y_transform = "none",
  chromosome_spacing = 1e+06,
  hyper_color = "#ff0000",
  hypo_color = "#008800",
  point_size = 1,
  point_alpha = 0.5,
  label_top_n = 10,
  label_size = 3,
  gap_frac = 0.04,
  connector_dx1 = NULL,
  connector_dx2 = NULL,
  connector_elbow = 0.8,
  connector_tilt_frac = 0.2
)

Arguments

dmr_file

DEG table from MethylKit analysis.

gff_file

Genomic structural annotation GFF3/GTF file path. If provided and label_col is NULL, will try to label by overlapped/nearest gene_id.

format

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

gene_table

Optional gene ID/name mapping table (first two columns: id, name). If provided, will use gene name for labels when possible.

label_type

Label by gene name or gene id. ("name", "id"). If "name" but no gene names can be inferred from gff_file, please provide gene_table.

label_col

Column name used for annotation labels. If NULL, uses chr:start-end.

y_transform

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

chromosome_spacing

Gap width (bp) inserted between chromosomes on x-axis. (1e6).

hyper_color

Color for hyper-methylated points. ("#ff0000").

hypo_color

Color for hypo-methylated points. ("#008800").

point_size

Point size. (1).

point_alpha

Point alpha. (0.5).

label_top_n

Number of top positive and top negative DMGs to label. (10).

label_size

Text size for labels. (3).

gap_frac

Minimum vertical gap between labels (fraction of y-range). (0.04).

connector_dx1

First connector horizontal offset (bp). Default adapts to genome size.

connector_dx2

Second connector horizontal offset (bp). Default adapts to genome size.

connector_elbow

Scale factor applied to connector_dx2. (0.8).

connector_tilt_frac

Tilt amplitude for the second connector segment as a fraction of gap_frac. (0.2).

Value

A ggplot object of DMG manhattan plot.

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_manhattan(
  dmr_file = dmr_file,
  gff_file = gff_file,
  format = "auto",
  gene_table = NULL,
  label_type = "name",
  label_col = NULL,
  y_transform = "none",
  chromosome_spacing = 1e6,
  hyper_color = "#ff0000",
  hypo_color = "#008800",
  point_size = 1,
  point_alpha = 0.5,
  label_top_n = 10,
  label_size = 3,
  gap_frac = 0.04,
  connector_dx1 = NULL,
  connector_dx2 = NULL,
  connector_elbow = 0.8,
  connector_tilt_frac = 0.2
)
#> Import genomic features from the file as a GRanges object ... 
#> OK
#> Prepare the 'metadata' data frame ... 
#> OK
#> Make the TxDb object ... 
#> OK