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Plot gsMap (full & highlight) with robust color mapping

plot_gsMap.Rd

Main plotting function. Full panel uses per-annotation colors; highlight panel keeps all data but greys out non-highlighted levels.

Usage

plot_gsMap(
  path,
  width1 = 6,
  height1 = 4,
  width2 = 8,
  height2 = 4,
  color = NULL,
  anno_colors = NULL,
  reverse_x = FALSE,
  reverse_y = TRUE,
  save_folder = "./figure/gsmap/tmp",
  basename = NULL,
  traitname = NULL,
  highlight_tissue = NULL,
  highlight_color = NULL,
  other_grey = "grey60"
)

Arguments

path

CSV file path with columns: sx, sy, annotation, logp.

width1, height1

PDF size for full-annotation figure.

width2, height2

PDF size for combined highlight+logp figure.

color

Named color vector for annotations (fallback).

anno_colors

Preferred named color vector for annotations (partial allowed).

reverse_x, reverse_y

Reverse axes or not.

save_folder

Output folder.

basename

Optional plot basename.

traitname

Optional trait name.

highlight_tissue

Levels to highlight (default: first level if missing).

highlight_color

Highlight color (single string or named vector).

other_grey

Color used for non-highlight levels in highlight panel.

Examples

if (FALSE) { # \dontrun{
# Simulate & write a small CSV
set.seed(1)
df <- data.frame(sx = rnorm(60), sy = rnorm(60),
                 annotation = rep(c("Heart","Liver","Lung","Brain"), each = 15),
                 logp = runif(60, 1, 12))
fp <- file.path(tempdir(), "A_B_trait_gsMap_plot.csv")
write.csv(df, fp, row.names = FALSE)

# Partial colors; highlight Brain in gold; others grey
anno_cols <- c(Heart = "#E64B35FF", Liver = "#4DBBD5FF")
plot_gsMap(path = fp, width1 = 5, height1 = 3.5, width2 = 7, height2 = 3.5,
           anno_colors = anno_cols, reverse_x = FALSE, reverse_y = TRUE,
           save_folder = tempdir(), basename = "Demo.Base", traitname = "trait",
           highlight_tissue = "Brain", highlight_color = "#FFD700", other_grey = "grey60")
} # }