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das-versprechen-der-vernetzung.r
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library('igraph')
NFDI_edges <- read.table(header=TRUE,
sep=",",
text="
from,to
BERD@NFDI,KonsortSWD
BERD@NFDI,MaRDI
BERD@NFDI,NFDI4Memory
BERD@NFDI,Text+
DAPHNE4NFDI,FAIRmat
DAPHNE4NFDI,NFDI-MatWerk
DAPHNE4NFDI,NFDI4Cat
DAPHNE4NFDI,NFDI4Chem
DAPHNE4NFDI,NFDI4Health
DAPHNE4NFDI,NFDI4Ing
DAPHNE4NFDI,NFDI4Objects
DAPHNE4NFDI,PUNCH4NFDI
FAIRmat,DAPHNE4NFDI
FAIRmat,DataPLANT
FAIRmat,MaRDI
FAIRmat,NFDI-MatWerk
FAIRmat,NFDI4Cat
FAIRmat,NFDI4Chem
FAIRmat,NFDI4DataScience
FAIRmat,NFDI4Ing
FAIRmat,NFDIxCS
FAIRmat,PUNCH4NFDI
MaRDI,BERD@NFDI
MaRDI,FAIRmat
MaRDI,NFDI-MatWerk
MaRDI,NFDI-Neuro
MaRDI,NFDI4Cat
MaRDI,NFDI4Chem
MaRDI,NFDI4Ing
MaRDI,PUNCH4NFDI
NFDI-MatWerk,DAPHNE4NFDI
NFDI-MatWerk,DataPLANT
NFDI-MatWerk,FAIRmat
NFDI-MatWerk,MaRDI
NFDI-MatWerk,NFDI4Chem
NFDI-MatWerk,NFDI4DataScience
NFDI-MatWerk,NFDI4Ing
NFDI-MatWerk,NFDIxCS
NFDI-Neuro,DataPLANT
NFDI-Neuro,GHGA
NFDI-Neuro,NFDI4BioDiversity
NFDI-Neuro,NFDI4Culture
NFDI-Neuro,NFDI4Earth
NFDI-Neuro,NFDI4Health
NFDI-Neuro,NFDI4Ing
NFDI-Neuro,NFDI4Microbiota
NFDI4Agri,DataPLANT
NFDI4Agri,KonsortSWD
NFDI4Agri,NFDI4BioDiversity
NFDI4Agri,NFDI4Earth
NFDI4Agri,NFDI4Health
NFDI4Agri,NFDI4Immuno
NFDI4Agri,NFDI4Microbiota
NFDI4DataScience,KonsortSWD
NFDI4DataScience,MaRDI
NFDI4DataScience,NFDI-MatWerk
NFDI4DataScience,NFDI4BioDiversity
NFDI4DataScience,NFDI4Cat
NFDI4DataScience,NFDI4Chem
NFDI4DataScience,NFDI4Culture
NFDI4DataScience,NFDI4Health
NFDI4DataScience,NFDI4Ing
NFDI4DataScience,NFDI4Microbiota
NFDI4DataScience,NFDIxCS
NFDI4Earth,DataPLANT
NFDI4Earth,GHGA
NFDI4Earth,KonsortSWD
NFDI4Earth,NFDI4Agri
NFDI4Earth,NFDI4BioDiversity
NFDI4Earth,NFDI4Cat
NFDI4Earth,NFDI4Chem
NFDI4Earth,NFDI4Culture
NFDI4Earth,NFDI4Health
NFDI4Earth,NFDI4Ing
NFDI4Earth,NFDI4Objects
NFDI4Immuno,GHGA
NFDI4Immuno,NFDI4Agri
NFDI4Immuno,NFDI4Health
NFDI4Immuno,NFDI4Microbiota
NFDI4Memory,BERD@NFDI
NFDI4Memory,KonsortSWD
NFDI4Memory,MaRDI
NFDI4Memory,NFDI4Culture
NFDI4Memory,NFDI4Objects
NFDI4Memory,Text+
NFDI4Microbiota,DataPLANT
NFDI4Microbiota,GHGA
NFDI4Microbiota,NFDI4Agri
NFDI4Microbiota,NFDI4BioDiversity
NFDI4Microbiota,NFDI4Chem
NFDI4Microbiota,NFDI4DataScience
NFDI4Microbiota,NFDI4Health
NFDI4Microbiota,NFDI4Immuno
NFDI4Microbiota,NFDI4Ing
NFDI4Objects,KonsortSWD
NFDI4Objects,NFDI4Agri
NFDI4Objects,NFDI4BioDiversity
NFDI4Objects,NFDI4Culture
NFDI4Objects,NFDI4Earth
NFDI4Objects,NFDI4Memory
NFDI4Objects,Text+
NFDI4SD,NFDI4Culture
NFDI4SD,NFDI4DataScience
NFDI4SD,NFDI4Memory
NFDI4SD,NFDI4Objects
NFDIxCS,FAIRmat
NFDIxCS,MaRDI
NFDIxCS,NFDI4Chem
NFDIxCS,NFDI4DataScience
NFDIxCS,NFDI4Earth
NFDIxCS,NFDI4Ing
PUNCH4NFDI,DAPHNE4NFDI
PUNCH4NFDI,FAIRmat
PUNCH4NFDI,GHGA
PUNCH4NFDI,MaRDI
PUNCH4NFDI,NFDI4Earth
PUNCH4NFDI,NFDI4Ing
PUNCH4NFDI,NFDIxCS
Text+,KonsortSWD
Text+,NFDI4BioDiversity
Text+,NFDI4Culture
Text+,NFDI4Earth
Text+,NFDI4Ing
Text+,NFDI4Memory
Text+,NFDI4Objects
")
NFDI_network <- graph_from_data_frame(NFDI_edges,
directed=FALSE
)
set.seed(1234)
plot(NFDI_network, # loading data frame
main = "NFDI-Netzwerk", # adding a title
frame = TRUE # making a frame
)
set.seed(1234)
plot(NFDI_network, # loading data frame
main = "NFDI-Netzwerk", # adding a title
frame = TRUE, # making a frame
layout = layout.graphopt, #* better layout options
)
set.seed(1234)
plot(NFDI_network, # loading data frame
main = "NFDI-Netzwerk", # adding a title
frame = TRUE, # making a frame
layout = layout.graphopt, # better layout options
vertex.color = "#ffcc66", #* color of nodes
vertex.frame.color = "#ffcc66", #* color of the frame of nodes
vertex.label.cex = 0.5, #* size of the description of the labels
vertex.label.color = "black", #* color of the description
edge.color = "#808080", #* color of edges
edge.curved = 0.1, #* factor of "curvity"
)
degree(NFDI_network) #* calculate number of edges
set.seed(1234)
plot(NFDI_network, # loading data frame
main = "NFDI-Netzwerk", # adding a title
frame = TRUE, # making a frame
layout = layout.graphopt, # better layout options
vertex.color = "#ffcc66", # color of nodes
vertex.frame.color = "#ffcc66", # color of the frame of nodes
vertex.label.cex = 0.5, # size of the description of the labels
vertex.label.color = "black", # color of the description
# color: https://www.w3schools.com/colors/colors_picker.asp
edge.color = "#808080", # color of edges
edge.curved = 0.1, # factor of "curvity"
vertex.size = degree(NFDI_network), #* size of nodes depends on amount of edges
)
NFDI_network_directed <- graph_from_data_frame(NFDI_edges,
directed = TRUE
)
set.seed(1234)
plot(NFDI_network_directed, #<<<<<<< loading data frame
main = "NFDI-Netzwerk", # adding a title
frame = TRUE, # making a frame
layout = layout.graphopt, # better layout options
vertex.color = "#ffcc66", # color of nodes
vertex.frame.color = "#ffcc66", # color of the frame of nodes
vertex.label.cex = 0.5, # size of the description of the labels
vertex.label.color = "black", # color of the description
# color: https://www.w3schools.com/colors/colors_picker.asp
edge.color = "#808080", # color of edges
edge.curved = 0, #<<<<<<<<< factor of "curvity"
vertex.size = degree(NFDI_network_directed), #<<<<<< size of nodes depends on amount of edges
edge.arrow.size = .5, #* arrow size, defaults to 1
)
degree(NFDI_network_directed,
mode = "in")
set.seed(1234)
plot(NFDI_network_directed, # loading data frame
main = "NFDI-Netzwerk (<in>)", #<<<<<<<< adding a title
frame = TRUE, # making a frame
layout = layout.graphopt, # better layout options
vertex.color = "#ffcc66", # color of nodes
vertex.frame.color = "#ffcc66", # color of the frame of nodes
vertex.label.cex = 0.5, # size of the description of the labels
vertex.label.color = "black", # color of the description
# color: https://www.w3schools.com/colors/colors_picker.asp
edge.color = "#808080", # color of edges
edge.curved = 0, # factor of "curvity"
vertex.size = degree(NFDI_network_directed,
mode = "in"), #<<<<<< size of nodes depends on amount of edges
edge.arrow.size = .5, # arrow size, defaults to 1
)
degree(NFDI_network_directed,
mode = "out")
set.seed(1234)
plot(NFDI_network_directed, # loading data frame
main = "NFDI-Netzwerk (<out>)", #<<<<<<<< adding a title
frame = TRUE, # making a frame
layout = layout.graphopt, # better layout options
vertex.color = "#ffcc66", # color of nodes
vertex.frame.color = "#ffcc66", # color of the frame of nodes
vertex.label.cex = 0.5, # size of the description of the labels
vertex.label.color = "black", # color of the description
# color: https://www.w3schools.com/colors/colors_picker.asp
edge.color = "#808080", # color of edges
edge.curved = 0, # factor of "curvity"
vertex.size = degree(NFDI_network_directed,
mode = "out"), #<<<<<< size of nodes depends on amount of edges
edge.arrow.size = .5, # arrow size, defaults to 1
)
NFDI_network_directed_filter <- delete_vertices(NFDI_network_directed,
V(NFDI_network_directed)[ degree(NFDI_network_directed, mode = "out") == 0 ])
degree(NFDI_network_directed_filter,
mode = "total")
set.seed(1234)
plot(NFDI_network_directed_filter, #<<<<<<<< loading data frame
main = "NFDI-Netzwerk (<filtered>)", #<<<<<<<< adding a title
frame = TRUE, # making a frame
layout = layout.graphopt, # better layout options
vertex.color = "#ffcc66", # color of nodes
vertex.frame.color = "#ffcc66", # color of the frame of nodes
vertex.label.cex = 0.5, # size of the description of the labels
vertex.label.color = "black", # color of the description
# color: https://www.w3schools.com/colors/colors_picker.asp
edge.color = "#808080", # color of edges
edge.curved = 0, # factor of "curvity"
vertex.size = degree(NFDI_network_directed_filter,
mode = "total"), #<<<<<< size of nodes depends on amount of edges
edge.arrow.size = .5, # arrow size, defaults to 1
)
NFDI_nodes <- read.table(header=TRUE,
sep=",",
text="
name,group
BERD@NFDI,3
DAPHNE4NFDI,5
DataPLANT,2
FAIRmat,5
GHGA,1
KonsortSWD,3
MaRDI,4
NFDI-MatWerk,4
NFDI-Neuro,1
NFDI4Agri,2
NFDI4BioDiversity,2
NFDI4Cat,5
NFDI4Chem,5
NFDI4Culture,3
NFDI4DataScience,4
NFDI4Earth,2
NFDI4Health,1
NFDI4Immuno,1
NFDI4Ing,4
NFDI4Memory,3
NFDI4Microbiota,2
NFDI4Objects,3
NFDI4SD,3
NFDIxCS,4
PUNCH4NFDI,5
Text+,3
")
NFDI_network_directed <- graph_from_data_frame(d = NFDI_edges, # d = data frame =~ edges
vertices = NFDI_nodes, #nodes
directed = TRUE) #directed
NFDI_color_code <- c("#f5ac9f", # Medizin
"#e43516", # Lebenswissenschaften
"#f9b900", # Geisteswissenschaften
"#007aaf", # Ingenieurwissenschaften
"#6ca11d" # Chemie/Physik
)
NFDI_color_groups <- NFDI_color_code[as.numeric(as.factor(V(NFDI_network_directed)$group))]
set.seed(1234)
plot(NFDI_network_directed, # loading data frame
main = "NFDI-Netzwerk (<Konferenzsystematik>)", #<<<<<<<< adding a title
frame = TRUE, # making a frame
layout = layout.graphopt, # better layout options
vertex.color = NFDI_color_groups, #<<<<<<<<<< color of nodes
vertex.frame.color = NFDI_color_groups, #<<<<<<<<<< color of the frame of nodes
vertex.label.cex = 0.5, # size of the description of the labels
vertex.label.color = "black", # color of the description
# color: https://www.w3schools.com/colors/colors_picker.asp
edge.color = "#808080", # color of edges
edge.curved = 0, # factor of "curvity"
vertex.size = degree(NFDI_network_directed,
mode = "total"), #<<<<<<<<<<< size of nodes depends on amount of edges
edge.arrow.size = .5, # arrow size, defaults to 1
)
legend("bottomright", # x-position
title = "NFDI-Konferenzsystematik", # title
legend = c(
"(1) Medizin",
"(2) Lebenswissenschaften",
"(3) Geisteswissenschaften",
"(4) Ingenieurwissenschaften",
"(5) Chemie/Physik"
), # the text of the legend
col = NFDI_color_code , # colors of lines and points beside the legend text
pch = 20, # the plotting symbols appearing in the legend
bty = "n", # no frame, the type of box to be drawn around the legend (n=no frame)
cex = .75, # character expansion factor relative to current par("cex").
pt.cex = 2 # expansion factor(s) for the points
)
set.seed(1234)
NFDI_network_directed_cluster <- cluster_optimal(NFDI_network_directed)
plot(NFDI_network_directed_cluster, #<<<<<<<<<<< clustered network data
NFDI_network_directed, # loading data frame
main = "NFDI-Netzwerk (<Konferenzsystematik>)", # adding a title
frame = TRUE, # making a frame
layout = layout.graphopt, # better layout options
#vertex.color = NFDI_color_groups, #<<<<<<<<<< color of nodes
vertex.frame.color = NFDI_color_groups, #<<<<<<<<<< color of the frame of nodes
vertex.label.cex = 0.5, # size of the description of the labels
vertex.label.color = "black", # color of the description
# color: https://www.w3schools.com/colors/colors_picker.asp
edge.color = NA, #<<<<<<<<<<<<<< color of edges
edge.curved = 0, # factor of "curvity"
vertex.size = degree(NFDI_network_directed,
mode = "total"), #<<<<<<<<<<< size of nodes depends on amount of edges
edge.arrow.size = .5, # arrow size, defaults to 1
col = NFDI_color_groups, #<<<<<<<<<<<<< color of nodes
mark.col = "grey", #<<<<<<<<<< color groups
mark.border = NA, #<<<<<<<<<< no border color
)
legend("bottomright", # x-position
title = "NFDI-Konferenzsystematik", # title
legend = c(
"(1) Medizin",
"(2) Lebenswissenschaften",
"(3) Geisteswissenschaften",
"(4) Ingenieurwissenschaften",
"(5) Chemie/Physik"
), # the text of the legend
col = NFDI_color_code , # colors of lines and points beside the legend text
pch = 20, # the plotting symbols appearing in the legend
bty = "n", # no frame, the type of box to be drawn around the legend (n=no frame)
cex = .75, # character expansion factor relative to current par("cex").
pt.cex = 2 # expansion factor(s) for the points
)
set.seed(1234)
plot(NFDI_network_directed_cluster, # clustered network data
NFDI_network_directed, # loading data frame
main = "NFDI-Netzwerk (<Konferenzsystematik>)", # adding a title
frame = TRUE, # making a frame
layout = layout.graphopt, # better layout options
vertex.frame.color = NFDI_color_groups, # color of the frame of nodes
vertex.label.cex = 0.5, # size of the description of the labels
vertex.label.color = "black", # color of the description
# color: https://www.w3schools.com/colors/colors_picker.asp
edge.color = c(NA, "#bf4040")[crossing(NFDI_network_directed_cluster, NFDI_network_directed) + 1],
#<<<<<<<<<<<<<<<<< show only edges if they go to another group
edge.curved = 0, # factor of "curvity"
vertex.size = degree(NFDI_network_directed,
mode = "total"), #<<<<<<<<<<< size of nodes depends on amount of edges
edge.arrow.size = .5, # arrow size, defaults to 1
col = NFDI_color_groups, # color of nodes
mark.col = "grey", # color groups
mark.border = NA, # no border color
)
legend("bottomright", # x-position
title = "NFDI-Konferenzsystematik", # title
legend = c(
"(1) Medizin",
"(2) Lebenswissenschaften",
"(3) Geisteswissenschaften",
"(4) Ingenieurwissenschaften",
"(5) Chemie/Physik"
), # the text of the legend
col = NFDI_color_code , # colors of lines and points beside the legend text
pch = 20, # the plotting symbols appearing in the legend
bty = "n", # no frame, the type of box to be drawn around the legend (n=no frame)
cex = .75, # character expansion factor relative to current par("cex").
pt.cex = 2 # expansion factor(s) for the points
)