draw_map2 function

Draw a linkage map

Provides a simple draw of a linkage map.

draw_map2(
  ...,
  tag = NULL,
  id = TRUE,
  pos = TRUE,
  cex.label = NULL,
  main = NULL,
  group.names = NULL,
  centered = FALSE,
  y.axis = TRUE,
  space = NULL,
  col.group = NULL,
  col.mark = NULL,
  col.tag = NULL,
  output = NULL,
  verbose = TRUE
)

Arguments

• ...: map(s). Object(s) of class sequence and/or data.frame. If data.frame, it must have two columns: column 1: marker id; column 2: position (cM) (numeric).
• tag: name(s) of the marker(s) to highlight. If "all", all markers will be highlighted. Default is NULL.
• id: logical. If TRUE (default), shows name(s) of tagged marker(s).
• pos: logical. If TRUE (default), shows position(s) of tagged marker(s).
• cex.label: the magnification used for label(s) of tagged marker(s). If NULL (default), the cex will be automatically calculated to avoid overlapping.
• main: an overall title for the plot. Default is NULL.
• group.names: name(s) to identify the group(s). If NULL (default), the name(s) of the sequence(s) will be used.
• centered: logical. If TRUE, the group(s) will be aligned in the center. If FALSE (default), the group(s) will be aligned at the top.
• y.axis: logical. If TRUE (default), shows y axis. If centered = TRUE, the y axis will always be hidden.
• space: numerical. Spacing between groups. If NULL (default), the spacing will be automatically calculated to avoid overlapping.
• col.group: the color used for group(s).
• col.mark: the color used for marker(s).
• col.tag: the color used for highlighted marker(s) and its/theirs label(s).
• output: the name of the output file. The file format can be specified by adding its extension. Available formats: 'bmp', 'jpeg', 'png', 'tiff', 'pdf' and 'eps' (default).
• verbose: If TRUE, print tracing information.

Returns

ggplot graphic with genetic map draw

Examples

data("onemap_example_out")
twopt <- rf_2pts(onemap_example_out)
lg<-group(make_seq(twopt, "all"))
seq1<-make_seq(order_seq(input.seq= make_seq(lg,1),twopt.alg = "rcd"), "force")
seq2<-make_seq(order_seq(input.seq= make_seq(lg,2),twopt.alg = "rcd"), "force")
seq3<-make_seq(order_seq(input.seq= make_seq(lg,3),twopt.alg = "rcd"), "force")
draw_map2(seq1,seq2,seq3,tag = c("M1","M2","M3","M4","M5"),
output = paste0(tempfile(), ".png"))

Author(s)

Getulio Caixeta Ferreira, getulio.caifer@gmail.com