plot_map: Plot linkage maps
In mdavy86/polymapR: Linkage Analysis in Outcrossing Polyploids

Makes a simple plot of a list of generated linkage maps

plot_map(maplist, highlight = NULL, bg_col = "grey",
  highlight_col = "yellow", colname_in_mark = NULL,
  colname_beside_mark = NULL, palette_in_mark = colorRampPalette(c("white",
  "purple")), palette_beside_mark = colorRampPalette(c("white", "green")),
  color_by_type = FALSE, dosage_matrix = NULL, legend = FALSE,
  legend.x = 1, legend.y = 120, ...)

`maplist`	A list of maps. In the first column marker names and in the second their position.
`highlight`	A list of the same length of maplist with vectors of length 2 that specifies the limits in cM from and to which the plotted chromosomes should be highlighted.
`bg_col`	The background colour of the map.
`highlight_col`	The color of the highlight. Only used if `highlight` is specified.
`colname_in_mark`	Optional. The column name of the value to be plotted as marker color.
`colname_beside_mark`	Optional. The column name of the value to be plotted beside the markers.
`palette_in_mark, palette_beside_mark`	Color palette used to plot values. Only used if colnames of the values are specified.
`color_by_type`	Logical. Should the markers be coloured by type? If TRUE, dosage_matrix should be specified.
`dosage_matrix`	Optional (by default `NULL`). Dosage matrix of marker genotypes, input of `linkage`
`legend`	Logical. Should a legend be drawn?
`legend.x`	Optional. The x value of the coordinates of the legend.
`legend.y`	Optional. The y value of the coordinates of the legend.
`...`	Arguments passed to `plot`

data("maplist_P1")
plot_map(maplist = maplist_P1, colname_in_mark = "nnfit", bg_col = "white",
         palette_in_mark = colorRampPalette(c("blue", "purple", "red")),
         highlight = list(c(20, 60),
         c(60,80),
         c(20,30),
         c(40,70),
         c(60,80)))