onemap (version 2.1.2)

rf_graph_table: Plots pairwise recombination fractions and LOD Scores in a heatmap

Description

Plots a matrix of pairwise recombination fraction or LOD Scores using a color scale. Any value of the matrix can be easily accessed using an interactive plotly-html interface, helping users to check for possible problems.

Usage

rf_graph_table(input.seq, graph.LOD = FALSE, main = NULL,
  inter = FALSE, html.file = NULL, mrk.axis = "numbers",
  lab.xy = NULL, n.colors = 4)

Arguments

input.seq

an object of class sequence with a predefined order.

graph.LOD

logical. If TRUE, displays the LOD heatmap, otherwise, displays the recombination fraction heatmap.

main

character. The title of the plot.

inter

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

html.file

character naming the html file with iterative graphic.

mrk.axis

character, "names" to display marker names in the axis, "numbers" to display marker numbers and "none" to display axis free of labels.

lab.xy

character vector with length 2, first component is the label of x axis and second of the y axis.

n.colors

integer. Number of colors in the pallete.

Details

The color scale varies from red (small distances or big LODs) to purple. When hover on a cell, a dialog box is displayed with some information about corresponding markers for that cell (line (y) \(\times\) column (x)). They 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 is impossible to calculate recombination fraction via two-point analysis and, therefore, the corresponding cell will be empty (white color). 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.

Examples

# NOT RUN {
# }
# NOT RUN {
##outcross example
  data(onemap_example_out)
  twopt <- rf_2pts(onemap_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 plotly
  rf_graph_table(LG1.rcd, inter=TRUE, html.file= "LG1.rcd.html")

  ##F2 example
  data(onemap_example_f2)
  twopt <- rf_2pts(onemap_example_f2)
  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
  require(gridExtra)
  plot1 <- rf_graph_table(maps.list[[1]], main="Group 1",inter=FALSE)
  plot2 <- rf_graph_table(maps.list[[2]], main="Group 2",inter=FALSE)
  plot3 <- rf_graph_table(maps.list[[3]], main="Group 3",inter=FALSE)
  grid.arrange(plot1, plot2, plot3, nrow=3)
# }