rf.graph.table {onemap} | R Documentation |
Plots a matrix of pairwise recombination fractions (under the diagonal) and LOD Scores (upper the diagonal) using a color scale. Any value of the matrix can be easily accessed using an interactive Tcl-Tk interface, helping the user to check for possible problems.
rf.graph.table(input.seq, scale=1, axis.cex=1, main, inter=TRUE)
input.seq |
an object of class |
scale |
controls the plot size. If |
axis.cex |
the magnification to be used for axis annotation. |
main |
the title for no interactive plot, i.e. it is only
used if |
inter |
logical. If |
The color scale varies from red (small distances or big LODs) 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 on the data set; 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 analysis and, therefore the corresponding cell will be
empty. For cells on the diagonal of the matrix, 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@usp.br
##outcross example 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) ##F2 example data(fake.f2.onemap) twopt <- rf.2pts(fake.f2.onemap) all.mark <- make.seq(twopt,"all") groups <- group(all.mark) ##"pre-allocate" an empty list of length groups$n.groups (3, in this case) maps.list<-vector("list", groups$n.groups) for(i in 1:groups$n.groups){ ##create linkage group i LG.cur <- make.seq(groups,i) ##ordering map.cur<-order.seq(LG.cur, subset.search = "sample") ##assign the map of the i-th group to the maps.list maps.list[[i]]<-make.seq(map.cur, "force") } ##Plot LOD/recombination fraction matrices for each group op <- par(mfrow = c(1, 3)) for(i in 1:groups$n.groups) rf.graph.table(maps.list[[i]], axis.cex=.7, main=paste("Group", i),inter=FALSE) par(op) ## End(Not run)