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Plot differentially expressed genes (DEGs) hyper/hypo distributions by chromosome

Source: R/plot_deg_chrom.R
plot_deg_chrom.Rd

Plot differentially expressed genes (DEGs) hyper/hypo distributions by chromosomes.

Usage

plot_deg_chrom(
  deg_file,
  gff_file,
  format = "auto",
  id_col = "GeneID",
  fc_col = "log2FoldChange",
  violin_scale = "count",
  violin_border = 0.5,
  point_shape = 16,
  point_size = 2,
  jitter_width = 0.2,
  hyper_color = "#ff000088",
  hypo_color = "#00880088"
)

Arguments

deg_file

DEG table from DESeq2 analysis.

gff_file

Genomic structural annotation GFF3/GTF file path.

format

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

id_col

Gene IDs column name. ("GeneID").

fc_col

Log2(fold change) column name. ("log2FoldChange").

violin_scale

Violin scale mode. ("count", "area", "width").

violin_border

Violin border width. (0.5).

point_shape

Points shape (0-25). (16).

point_size

Point size. (2).

jitter_width

Horizontal jitter width. (0.2).

hyper_color

Color for up-regulated points. ("#ff000088").

hypo_color

Color for down-regulated points. ("#00880088").

Value

A ggplot object of chromosome-wise DEG distributions.

Examples

# DEG results from DESeq2
deg_file <- system.file(
    "extdata",
    "example.deg",
    package = "GAnnoViz")

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

# Plot
plot_deg_chrom(
  deg_file = deg_file,
  gff_file = gff_file,
  format = "auto",
  id_col = "GeneID",
  fc_col = "log2FoldChange",
  violin_scale = "count",
  violin_border = 0.5,
  point_shape = 16,
  point_size = 2,
  jitter_width = 0.2,
  hyper_color = "#ff000088",
  hypo_color = "#00880088"
)
#> Import genomic features from the file as a GRanges object ... 
#> OK
#> Prepare the 'metadata' data frame ... 
#> OK
#> Make the TxDb object ... 
#> OK