onemap (version 1.0-0)

rf.graph.table: Plots a pairwise recombination fraction matrix using a color scale.

Description

Plots a pairwise recombination fraction matrix using a color scale. Values of interest can be accessed using an interactive Tcl-Tk interface.

Usage

rf.graph.table(w, scale=1, axis.cex=1, inter=TRUE)

Arguments

w

an object of class sequence with a predefined order.

scale

controls the plot size. If inter == FALSE this value is not used.

axis.cex

the magnification to be used for axis annotation.

inter

logical. If TRUE, an interactive graphic is plotted. Otherwise, a default graphic device is used.

Details

The color scale varies from red (small distances) to dark blue. When clicking on a cell, a dialog box is displayed with some information about corresponding markers for that cell (line $\times$ column). The informations are: $i$) the name of the markers; $ii$) the number of the markers; $iii$) the segregation types; $iv$) the recombination fraction between the markers and $v$) the LOD-Score for each possible linkage phase calculated via two-point analysis. For neighbor markers, the multipoint recombination fraction is printed; otherwise, the two-point recombination fraction is printed. For markers of type D1 and D2, it's impossible to calculate recombination fraction via two-point, therefore the corresponding cell will be empty. For diagonal cells, the name, the number and the type of the marker are printed, as well as the percentage of missing data for that marker.

Examples

data(example_out)
  twopt <- rf.2pts(example_out)
  all.mark <- make.seq(twopt,"all")
  groups <- group(all.mark)
  LG1 <- make.seq(groups,1)
  LG1.rcd <- rcd(LG1)
  rf.graph.table(LG1.rcd, inter=FALSE)
##Now, using interactive Tcl-Tk
  rf.graph.table(LG1.rcd, scale=1.5, inter=TRUE)