rf.graph.table {onemap} | R Documentation |
Plots a pairwise recombination fraction matrix using a color scale. Values of interest can be accessed using an interactive Tcl-Tk interface.
rf.graph.table(w, scale=1, axis.cex=1, inter=TRUE)
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. |
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.
Marcelo Mollinari, mmollina@esalq.usp.br
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) ## Not run: ##Now, using interactive Tcl-Tk rf.graph.table(LG1.rcd, scale=1.5, inter=TRUE) ## End(Not run)