draw_map2: Draw a linkage map

In onemap: Construction of Genetic Maps in Experimental Crosses

Draw a linkage map

Description

Provides a simple draw of a linkage map.

Usage

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.

Value

ggplot graphic with genetic map draw

Author(s)

Getulio Caixeta Ferreira, [e-mail]

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"))

onemap documentation built on Nov. 26, 2022, 9:05 a.m.