plot.data_network

[priviere]

• create a standard input format : look at shinemas2R::is.get.data.output.R and appendix D of the vignette of shinemas2R

• reformat code from shinemas2R functions

  • shinemas2R::get.ggplot.R & shinemas2R::get.ggplot_hide.labels.part.R that may be useful if we keep the format of the seed lots GERMPLASM_LOCATION_YEAR_DIGIT

  • shinemas2R::get.ggplot_plot.network.R and shinemas2R::get.ggplot_ggnet.custom.R
    But see https://briatte.github.io/ggnetwork/ => maybe better to go from here and
    forget shinemas2R::get.ggplot_plot.network.R and shinemas2R::get.ggplot_ggnet.custom.R functions ?

  • shinemas2R::get.ggplot_network.relation.barplot.R

  • shinemas2R::get.ggplot_network.relation.map.R

  • pie on network or map : reformat code from shinemas2R function shinemas2R::get.ggplot_pie.on.ggplot
    But maybe forgot it and look at other solutions :
    http://stackoverflow.com/questions/10368180/plotting-pie-graphs-on-map-in-ggplot
    http://rgraphgallery.blogspot.fr/2013/04/rg-plot-pie-over-google-map.html
    https://qdrsite.wordpress.com/2016/06/26/pies-on-a-map/

[priviere]

Following discussion with Mathieu :

• objective : have insight on what is going on in the network with simple graph

• format data

  • format 1
    id_event, seed_lot_parent, seed_lot_child, relation_type
    germplasm_parent, location_parent, year_parent,
    germplasm_son, location_son, year_son
    alt, long, lat
    => do a test with the four first columns with data
  • format 2
    id_event, relation_type
    germplasm_parent, location_parent, year_parent,
    germplasm_son, location_son, year_son
    alt, long, lat
    => do a test with the ? first columns with data

• function to format the data
  output = matrix with 0 and 1

  • format network for SL, unipartite = square matrix SL
  • format network for farmer, unipartite = square matrix farmer
  • format network for germplasm-farmer, bipartite = column : germplasm; row : farmer (ex: http://www.mnhn.fr/fr/recherche-expertise/actualites/pollinisation-plantes-altitude-mouches-prennent-relais-abeilles )

• arg organise-sl in shinemas2R : curve line and arrows for diffusion

• Distance matrix : leave it, too complexe to do some thing ok

• cf graph from igraph for description (to convert to ggplot2) : cf http://kateto.net/network-visualization

• vignette : take into account local, regional national organisation for network structure (exemple with filter on data_network)

[priviere]

Done in v0.23

• format data (cf improve format_data_PPBstats() #65): lots of evolution compared to what was written here => see code and doc (add arg vertex_type and network_type)

• Distance matrix : leave it, too complexe to do something ok

• create plot.network_data.R:

  • bipartite graph (ex: http://www.mnhn.fr/fr/recherche-expertise/actualites/pollinisation-plantes-altitude-mouches-prennent-relais-abeilles )
  • network representation of seed lots: shinemas2R::get.ggplot_plot.network.R and shinemas2R::get.ggplot_ggnet.custom.R
    see https://briatte.github.io/ggnetwork/

• seed lot graph:

  • change edges representation in a more visible way
  • arg organize_sl:
    • make compulsory:
      • the format for "seed_lot_parent" and "seed_lot_child" : GERMPLASM_LOCATION_YEAR_DIGIT to be ok with code
      • the format for relation type: "diffusion"
    • curve line and arrows for diffusion
    • add barplot as for shinemas2R::get.ggplot_network.relation.barplot.R

• bipartite graph:

  • change vertex type with location and germplasm
  • have an histogram with the number of edges the germplasm have with the location and vice versa
  • add barplot as for shinemas2R::get.ggplot_network.relation.barplot.R

Still to do

• add barplot for unipart network on location as for bipart network on germplasm and location

• implement map

  • shinemas2R::get.ggplot_network.relation.map.R
  • use OpenStreetMap in order to have all possible region, countries
  • look at ggmap

• add pie on map and network

  • pie on network or map : reformat code from shinemas2R function shinemas2R::get.ggplot_pie.on.ggplot
    But maybe forgot it and look at other solutions :
    http://stackoverflow.com/questions/10368180/plotting-pie-graphs-on-map-in-ggplot
    http://rgraphgallery.blogspot.fr/2013/04/rg-plot-pie-over-google-map.html
    https://qdrsite.wordpress.com/2016/06/26/pies-on-a-map/

• others

  • shinemas2R::get.ggplot.R & shinemas2R::get.ggplot_hide.labels.part.R that may be useful if we keep the format of the seed lots GERMPLASM_LOCATION_YEAR_DIGIT
  • cf graph from igraph for description (to convert to ggplot2) : cf http://kateto.net/network-visualization
  • add arg threshold of link (already done with igraph, see cluster)

[priviere]

Done in v0.24

• implement map with ggmap + update vignette
• implement pie on map and network + update vignette
• add barplot for unipart network on location + update vignette
• display in variable edges of the network for unipart sl on barplot
  • only if data_to_pie is NULL to avoid conflict if same name in edge and data_to_pie
• display in variable edges of the network for unipart sl on map with pies
• display output from unipart location on a map