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Plot genomic FST with Top-N gene annotations

Source: R/plot_snp_anno.R
plot_snp_anno.Rd

Plot genomic FST with Top-N gene annotations.

Usage

plot_snp_anno(
  fst_file,
  gff_file,
  format = "auto",
  chrom_id,
  top_n = 20,
  orientation = "vertical",
  smooth_span = 0.5,
  fst_color = "#0088ff",
  point_size = 1,
  point_alpha = 0.3,
  label_size = 3,
  connector_dx1 = 20000,
  connector_dx2 = 40000,
  gap_frac = 0.05
)

Arguments

fst_file

FST sliding window results. (CHROM, BIN_START, BIN_END, WEIGHTED_FST, N_VARIANTS.

gff_file

Path to GFF3/GTF file as input.

format

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

chrom_id

Chromosome identifier ("chr1").

top_n

Number of top genes to annotate. (20).

orientation

Coordinate orientation. ("vertical", "horizontal").

smooth_span

Span for local regression smoothing. (0.1).

fst_color

Point color for FST. ("#0088ff").

point_size

Point size. (1).

point_alpha

Point alpha. (0.3).

label_size

Text size for gene labels. (3).

connector_dx1

First connector horizontal offset (bp). (2e4).

connector_dx2

Second connector horizontal offset (bp). (4e4).

gap_frac

Minimum vertical gap between labels (fraction of FST range). (0.05).

Value

A ggplot object representing genomic FST with Top-N gene annotations.

Author

benben-miao

Examples

# Example data in GAnnoViz
fst_file <- system.file(
  "extdata",
  "example.fst",
  package = "GAnnoViz")

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

# Chromosome FST with Top-20 gene annotations on chr11
plot_snp_anno(
  fst_file = fst_file,
  gff_file = gff_file,
  format = "auto",
  chrom_id = "chr2",
  top_n = 20,
  orientation = "vertical",
  smooth_span = 0.5,
  fst_color = "#0088ff",
  point_size = 1,
  point_alpha = 0.3,
  label_size = 3,
  connector_dx1 = 2e4,
  connector_dx2 = 4e4,
  gap_frac = 0.05
)
#> Import genomic features from the file as a GRanges object ... 
#> OK
#> Prepare the 'metadata' data frame ... 
#> OK
#> Make the TxDb object ... 
#> OK
#> `geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'