2.4 Bipart network analysis

This section deals with bipart network that represents “which location has which germplasm which year”.

2.4.1 Steps with PPBstats

  • Format the data with format_data_PPBstats()
  • get descriptive plot with plot()

2.4.2 Format the data

The format required is a data frame with the following compulsory columns as factor: "germplasm", "location", "year". Possible options are : "long", "lat" to get map representation

Note that data frame with unipart network for seed lots format can also be used.

The format of the data are checked by the function format_data_PPBstats() with the following arguments :

  • type : "data_network"
  • network_part : "bipart"
  • vertex_type : c("germplasm", "location")

The function returns list of igraph object3 coming from igraph::graph_from_data_frame().

data(data_network_unipart_sl)
head(data_network_unipart_sl)
##          seed_lot_parent         seed_lot_child relation_type
## 1 germ-8_loc-1_2007_0001 germ-8_loc-1_2008_0001     selection
## 2 germ-8_loc-1_2008_0001 germ-8_loc-1_2009_0001  reproduction
## 3 germ-8_loc-1_2009_0001 germ-8_loc-2_2009_0001     diffusion
## 4 germ-8_loc-1_2008_0001 germ-8_loc-1_2009_0001     selection
## 5 germ-1_loc-1_2005_0001 germ-8_loc-1_2006_0001  reproduction
## 6 germ-6_loc-1_2005_0001 germ-8_loc-1_2006_0001  reproduction
##   relation_year_start relation_year_end germplasm_parent location_parent
## 1                2007              2008           germ-8           loc-1
## 2                2008              2009           germ-8           loc-1
## 3                2009              2009           germ-8           loc-1
## 4                2008              2009           germ-8           loc-1
## 5                2005              2006           germ-1           loc-1
## 6                2005              2006           germ-6           loc-1
##   year_parent alt_parent long_parent lat_parent germplasm_child
## 1        2007         50    0.616363   44.20314          germ-8
## 2        2008         50    0.616363   44.20314          germ-8
## 3        2009         50    0.616363   44.20314          germ-8
## 4        2008         50    0.616363   44.20314          germ-8
## 5        2005         50    0.616363   44.20314          germ-8
## 6        2005         50    0.616363   44.20314          germ-8
##   location_child year_child alt_child long_child lat_child
## 1          loc-1       2008        50   0.616363  44.20314
## 2          loc-1       2009        50   0.616363  44.20314
## 3          loc-2       2009       360   3.087025  45.77722
## 4          loc-1       2009        50   0.616363  44.20314
## 5          loc-1       2006        50   0.616363  44.20314
## 6          loc-1       2006        50   0.616363  44.20314
net_bipart = format_data_PPBstats(
  type = "data_network",
  data = data_network_unipart_sl, 
  network_part = "bipart", 
  vertex_type =  c("germplasm", "location")
  )
## data has been formated for PPBstats functions.

For bipart network, it returns a list with as many elements as year in the data as well as all years merged in the first element of the list. If no year are provided into the data, all information are merged.

names(net_bipart)
## [1] "2005-2006-2007-2008-2009" "2005"                    
## [3] "2006"                     "2007"                    
## [5] "2008"                     "2009"

2.4.3 Describe the data

The different representations are done with the plot() function.

p_net = plot(net_bipart, plot_type = "network", 
                          labels_on = TRUE, labels_size = 4)
names(p_net) # one element per year, the first element with all the data
## [1] "2005-2006-2007-2008-2009" "2005"                    
## [3] "2006"                     "2007"                    
## [5] "2008"                     "2009"
p_net$`2009`
## $network

With barplots, it represents the number of edges per vertex for each germplasm and each location.

p_bar = plot(net_bipart, plot_type = "barplot")
names(p_bar) # one element per year, the first element with all the data
## [1] "2005-2006-2007-2008-2009" "2005"                    
## [3] "2006"                     "2007"                    
## [5] "2008"                     "2009"
p_bar = p_bar$`2005-2006-2007-2008-2009`$barplot
p_bar$germplasm

p_bar$location

Location present on the network can be displayed on a map with plot_type = "map". When using map, do not forget to use credit : Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL.

p_map = PPBstats:::plot.data_network(net_bipart[1], plot_type = "map", labels_on = "location")
p_map$`2005-2006-2007-2008-2009`
## $map

As well as plot information regarding a variable on map with a pie with plot_type = "map" and by setting arguments data_to_pie and vec_variables:

# y1 is a quantitative variable
p_map_pies_y1 = PPBstats:::plot.data_network(net_bipart[1], data_to_pie, plot_type = "map", vec_variables = "y1")
p_map_pies_y1$`2005-2006-2007-2008-2009`
## $y1_map_with_pies

# y2 is a qualitative variable
p_map_pies_y2 = PPBstats:::plot.data_network(net_bipart[1], data_to_pie, plot_type = "map", vec_variables = "y2")
p_map_pies_y2$`2005-2006-2007-2008-2009`
## $y2_map_with_pies

  1. http://igraph.org/r/↩