rf_graph_table function

Plots pairwise recombination fractions and LOD Scores in a heatmap

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.

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

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 interative 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.
• display: logical. If inter TRUE and display TRUE interactive graphic is plotted in browser automatically when run the function

Returns

a ggplot graphic

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

##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)

  ##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")
  }

Author(s)

Rodrigo Amadeu, rramadeu@gmail.com