4 Get network information
Once the graph object is constructed, basic network information can be retrieved, and subnetworks can be extracted.
Load R Package
Example data
# Access built-in example datasets in ggNetView
# Relative abundance table of rarefied ASVs or OTUs
data("otu_rare_relative")
dim(otu_rare_relative)## [1] 2859 18
otu_rare_relative[1:5, 1:5]## KO1 KO2 KO3 KO4 KO5
## ASV_1 0.03306667 0.05453333 0.02013333 0.03613333 0.02686667
## ASV_2 0.05750000 0.03393333 0.06046667 0.05810000 0.07320000
## ASV_3 0.01733333 0.01296667 0.02290000 0.02336667 0.03106667
## ASV_4 0.04266667 0.01093333 0.01416667 0.01933333 0.03346667
## ASV_6 0.02646667 0.01856667 0.02110000 0.02353333 0.03806667## [1] 2859 8
tax_tab[1:5, 1:5]## # A tibble: 5 × 5
## OTUID Kingdom Phylum Class Order
## <chr> <chr> <chr> <chr> <chr>
## 1 ASV_2 Archaea Thaumarchaeota Unassigned Nitrososphaerales
## 2 ASV_3 Bacteria Verrucomicrobia Spartobacteria Unassigned
## 3 ASV_31 Bacteria Actinobacteria Actinobacteria Actinomycetales
## 4 ASV_27 Archaea Thaumarchaeota Unassigned Nitrososphaerales
## 5 ASV_9 Bacteria Unassigned Unassigned UnassignedBuild graph object
graph_obj <- build_graph_from_mat(
mat = otu_rare_relative,
transfrom.method = "none", # based your input data
r.threshold = 0.7,
p.threshold = 0.05,
method = "WGCNA",
cor.method = "pearson",
proc = "bonferroni",
module.method = "Fast_greedy",
node_annotation = tax_tab,
top_modules = 15,
seed = 1115
)
graph_obj## # A tbl_graph: 213 nodes and 844 edges
## #
## # An undirected simple graph with 29 components
## #
## # Node Data: 213 × 14 (active)
## name modularity modularity2 modularity3 Modularity Degree Strength Kingdom
## <chr> <fct> <ord> <chr> <ord> <dbl> <dbl> <chr>
## 1 ASV_649 5 5 5 5 27 26.5 Bacter…
## 2 ASV_705 5 5 5 5 27 26.5 Bacter…
## 3 ASV_12… 5 5 5 5 27 26.5 Bacter…
## 4 ASV_13… 5 5 5 5 27 26.5 Bacter…
## 5 ASV_14… 5 5 5 5 27 26.5 Bacter…
## 6 ASV_14… 5 5 5 5 27 26.5 Bacter…
## 7 ASV_24… 5 5 5 5 27 26.5 Bacter…
## 8 ASV_25… 5 5 5 5 27 26.4 Bacter…
## 9 ASV_28… 5 5 5 5 27 26.5 Bacter…
## 10 ASV_28… 5 5 5 5 27 26.5 Bacter…
## # ℹ 203 more rows
## # ℹ 6 more variables: Phylum <chr>, Class <chr>, Order <chr>, Family <chr>,
## # Genus <chr>, Species <chr>
## #
## # Edge Data: 844 × 5
## from to weight correlation corr_direction
## <int> <int> <dbl> <dbl> <chr>
## 1 194 195 0.959 0.959 Positive
## 2 185 208 0.954 0.954 Positive
## 3 185 213 0.957 0.957 Positive
## # ℹ 841 more rows4.1 Full-network information
graph_obj_info <- get_info_from_graph(graph_obj = graph_obj)
# return a list
class(graph_obj_info)## [1] "list"
names(graph_obj_info)## [1] "node_info" "edge_info"
graph_obj_info$node_info## # A tibble: 213 × 11
## name Modularity Degree Strength Kingdom Phylum Class Order Family Genus
## <chr> <ord> <dbl> <dbl> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 ASV_649 5 27 26.5 Bacteria Proteo… Alph… Rhiz… Unass… Unas…
## 2 ASV_705 5 27 26.5 Bacteria Actino… Acti… Acti… Cellu… Cell…
## 3 ASV_1234 5 27 26.5 Bacteria Gemmat… Gemm… Gemm… Gemma… Gemm…
## 4 ASV_1373 5 27 26.5 Bacteria Actino… Acti… Soli… Solir… Soli…
## 5 ASV_1479 5 27 26.5 Bacteria Verruc… Spar… Unas… Unass… Spar…
## 6 ASV_1481 5 27 26.5 Bacteria Proteo… Gamm… Unas… Unass… Unas…
## 7 ASV_2453 5 27 26.5 Bacteria Bacter… Sphi… Sphi… Chiti… Unas…
## 8 ASV_2562 5 27 26.4 Bacteria Bacter… Sphi… Sphi… Chiti… Unas…
## 9 ASV_2848 5 27 26.5 Bacteria Planct… Plan… Plan… Planc… Unas…
## 10 ASV_2844 5 27 26.5 Bacteria Proteo… Unas… Unas… Unass… Unas…
## # ℹ 203 more rows
## # ℹ 1 more variable: Species <chr>
graph_obj_info$edge_info## # A tibble: 844 × 5
## from to weight correlation corr_direction
## <chr> <chr> <dbl> <dbl> <chr>
## 1 ASV_6 ASV_39 0.959 0.959 Positive
## 2 ASV_20 ASV_1852 0.954 0.954 Positive
## 3 ASV_20 ASV_2911 0.957 0.957 Positive
## 4 ASV_172 ASV_43 0.969 0.969 Positive
## 5 ASV_614 ASV_65 0.943 0.943 Positive
## 6 ASV_69 ASV_173 0.995 0.995 Positive
## 7 ASV_69 ASV_206 0.994 0.994 Positive
## 8 ASV_69 ASV_744 0.976 0.976 Positive
## 9 ASV_945 ASV_69 0.985 0.985 Positive
## 10 ASV_69 ASV_1418 0.975 0.975 Positive
## # ℹ 834 more rows4.2 Sub-network (modularity) information
subgraph_info <- get_subgraph(graph_obj = graph_obj,
select_module = NULL)## Module Number
## 1 5 31
## 2 2 24
## 3 8 22
## 4 21 15
## 5 1 13
## 6 3 11
## 7 4 11
## 8 6 11
## 9 25 8
## 10 7 6
## 11 12 5
## 12 22 5
## 13 10 4
## 14 11 4
## 15 15 4
## 16 Others 39
# return a list
class(subgraph_info)## [1] "list"
names(subgraph_info)## [1] "sub_graph_all" "stat_module" "sub_graph_select"
subgraph_info$stat_module## Module Number
## 1 5 31
## 2 2 24
## 3 8 22
## 4 21 15
## 5 1 13
## 6 3 11
## 7 4 11
## 8 6 11
## 9 25 8
## 10 7 6
## 11 12 5
## 12 22 5
## 13 10 4
## 14 11 4
## 15 15 4
## 16 Others 39
subgraph_info$sub_graph_all## $`5`
## # A tbl_graph: 31 nodes and 330 edges
## #
## # An undirected simple graph with 1 component
## #
## # Node Data: 31 × 14 (active)
## name modularity modularity2 modularity3 Modularity Degree Strength Kingdom
## <chr> <fct> <ord> <chr> <ord> <dbl> <dbl> <chr>
## 1 ASV_649 5 5 5 5 27 26.5 Bacter…
## 2 ASV_705 5 5 5 5 27 26.5 Bacter…
## 3 ASV_12… 5 5 5 5 27 26.5 Bacter…
## 4 ASV_13… 5 5 5 5 27 26.5 Bacter…
## 5 ASV_14… 5 5 5 5 27 26.5 Bacter…
## 6 ASV_14… 5 5 5 5 27 26.5 Bacter…
## 7 ASV_24… 5 5 5 5 27 26.5 Bacter…
## 8 ASV_25… 5 5 5 5 27 26.4 Bacter…
## 9 ASV_28… 5 5 5 5 27 26.5 Bacter…
## 10 ASV_28… 5 5 5 5 27 26.5 Bacter…
## # ℹ 21 more rows
## # ℹ 6 more variables: Phylum <chr>, Class <chr>, Order <chr>, Family <chr>,
## # Genus <chr>, Species <chr>
## #
## # Edge Data: 330 × 5
## from to weight correlation corr_direction
## <int> <int> <dbl> <dbl> <chr>
## 1 1 2 0.996 0.996 Positive
## 2 1 3 0.997 0.997 Positive
## 3 2 3 0.994 0.994 Positive
## # ℹ 327 more rows
##
## $`2`
## # A tbl_graph: 24 nodes and 121 edges
## #
## # An undirected simple graph with 1 component
## #
## # Node Data: 24 × 14 (active)
## name modularity modularity2 modularity3 Modularity Degree Strength Kingdom
## <chr> <fct> <ord> <chr> <ord> <dbl> <dbl> <chr>
## 1 ASV_671 2 2 2 2 18 17.5 Bacter…
## 2 ASV_18… 2 2 2 2 17 16.6 Bacter…
## 3 ASV_29… 2 2 2 2 17 16.6 Bacter…
## 4 ASV_568 2 2 2 2 16 15.6 Bacter…
## 5 ASV_10… 2 2 2 2 16 15.6 Bacter…
## 6 ASV_11… 2 2 2 2 16 15.6 Bacter…
## 7 ASV_24… 2 2 2 2 15 14.5 Bacter…
## 8 ASV_28… 2 2 2 2 14 13.5 Bacter…
## 9 ASV_15… 2 2 2 2 13 12.6 Bacter…
## 10 ASV_24… 2 2 2 2 13 12.5 Bacter…
## # ℹ 14 more rows
## # ℹ 6 more variables: Phylum <chr>, Class <chr>, Order <chr>, Family <chr>,
## # Genus <chr>, Species <chr>
## #
## # Edge Data: 121 × 5
## from to weight correlation corr_direction
## <int> <int> <dbl> <dbl> <chr>
## 1 1 2 0.991 0.991 Positive
## 2 1 3 0.992 0.992 Positive
## 3 2 3 0.996 0.996 Positive
## # ℹ 118 more rows
##
## $`8`
## # A tbl_graph: 22 nodes and 131 edges
## #
## # An undirected simple graph with 1 component
## #
## # Node Data: 22 × 14 (active)
## name modularity modularity2 modularity3 Modularity Degree Strength Kingdom
## <chr> <fct> <ord> <chr> <ord> <dbl> <dbl> <chr>
## 1 ASV_802 8 8 8 8 18 17.5 Bacter…
## 2 ASV_723 8 8 8 8 18 17.5 Bacter…
## 3 ASV_11… 8 8 8 8 18 17.6 Bacter…
## 4 ASV_29… 8 8 8 8 18 17.6 Bacter…
## 5 ASV_927 8 8 8 8 16 15.6 Bacter…
## 6 ASV_13… 8 8 8 8 16 15.5 Bacter…
## 7 ASV_29… 8 8 8 8 16 15.5 Bacter…
## 8 ASV_10… 8 8 8 8 15 14.4 Bacter…
## 9 ASV_13… 8 8 8 8 15 14.6 Bacter…
## 10 ASV_14… 8 8 8 8 15 14.7 Bacter…
## # ℹ 12 more rows
## # ℹ 6 more variables: Phylum <chr>, Class <chr>, Order <chr>, Family <chr>,
## # Genus <chr>, Species <chr>
## #
## # Edge Data: 131 × 5
## from to weight correlation corr_direction
## <int> <int> <dbl> <dbl> <chr>
## 1 1 2 0.990 0.990 Positive
## 2 1 3 0.993 0.993 Positive
## 3 2 3 0.997 0.997 Positive
## # ℹ 128 more rows
##
## $`21`
## # A tbl_graph: 15 nodes and 42 edges
## #
## # An undirected simple graph with 1 component
## #
## # Node Data: 15 × 14 (active)
## name modularity modularity2 modularity3 Modularity Degree Strength Kingdom
## <chr> <fct> <ord> <chr> <ord> <dbl> <dbl> <chr>
## 1 ASV_25… 21 21 21 21 13 12.5 Bacter…
## 2 ASV_27… 21 21 21 21 12 11.6 Bacter…
## 3 ASV_879 21 21 21 21 8 7.67 Bacter…
## 4 ASV_10… 21 21 21 21 6 5.76 Bacter…
## 5 ASV_16… 21 21 21 21 6 5.70 Bacter…
## 6 ASV_511 21 21 21 21 5 4.80 Bacter…
## 7 ASV_578 21 21 21 21 5 4.76 Bacter…
## 8 ASV_917 21 21 21 21 5 4.80 Bacter…
## 9 ASV_18… 21 21 21 21 5 4.81 Bacter…
## 10 ASV_70 21 21 21 21 4 3.82 Bacter…
## 11 ASV_13… 21 21 21 21 4 3.86 Bacter…
## 12 ASV_839 21 21 21 21 3 2.85 Bacter…
## 13 ASV_20… 21 21 21 21 3 2.86 Bacter…
## 14 ASV_21… 21 21 21 21 3 2.86 Bacter…
## 15 ASV_88 21 21 21 21 2 1.90 Bacter…
## # ℹ 6 more variables: Phylum <chr>, Class <chr>, Order <chr>, Family <chr>,
## # Genus <chr>, Species <chr>
## #
## # Edge Data: 42 × 5
## from to weight correlation corr_direction
## <int> <int> <dbl> <dbl> <chr>
## 1 1 2 0.986 0.986 Positive
## 2 1 3 0.973 0.973 Positive
## 3 2 3 0.976 0.976 Positive
## # ℹ 39 more rows
##
## $`1`
## # A tbl_graph: 13 nodes and 43 edges
## #
## # An undirected simple graph with 1 component
## #
## # Node Data: 13 × 14 (active)
## name modularity modularity2 modularity3 Modularity Degree Strength Kingdom
## <chr> <fct> <ord> <chr> <ord> <dbl> <dbl> <chr>
## 1 ASV_19… 1 1 1 1 9 8.86 Bacter…
## 2 ASV_15… 1 1 1 1 9 8.86 Bacter…
## 3 ASV_24… 1 1 1 1 9 8.87 Bacter…
## 4 ASV_20… 1 1 1 1 9 8.79 Bacter…
## 5 ASV_20… 1 1 1 1 9 8.87 Bacter…
## 6 ASV_26… 1 1 1 1 9 8.87 Unassi…
## 7 ASV_968 1 1 1 1 8 7.88 Bacter…
## 8 ASV_27… 1 1 1 1 8 7.73 Bacter…
## 9 ASV_161 1 1 1 1 7 6.80 Bacter…
## 10 ASV_25… 1 1 1 1 5 4.72 Bacter…
## 11 ASV_534 1 1 1 1 2 1.90 Bacter…
## 12 ASV_26… 1 1 1 1 1 0.944 Bacter…
## 13 ASV_29… 1 1 1 1 1 0.963 Bacter…
## # ℹ 6 more variables: Phylum <chr>, Class <chr>, Order <chr>, Family <chr>,
## # Genus <chr>, Species <chr>
## #
## # Edge Data: 43 × 5
## from to weight correlation corr_direction
## <int> <int> <dbl> <dbl> <chr>
## 1 1 2 0.998 0.998 Positive
## 2 1 3 0.999 0.999 Positive
## 3 2 3 1.000 1.000 Positive
## # ℹ 40 more rows
##
## $`3`
## # A tbl_graph: 11 nodes and 38 edges
## #
## # An undirected simple graph with 1 component
## #
## # Node Data: 11 × 14 (active)
## name modularity modularity2 modularity3 Modularity Degree Strength Kingdom
## <chr> <fct> <ord> <chr> <ord> <dbl> <dbl> <chr>
## 1 ASV_945 3 3 3 3 9 8.71 Bacter…
## 2 ASV_19… 3 3 3 3 9 8.72 Bacter…
## 3 ASV_69 3 3 3 3 8 7.85 Bacter…
## 4 ASV_173 3 3 3 3 8 7.87 Bacter…
## 5 ASV_206 3 3 3 3 8 7.83 Bacter…
## 6 ASV_744 3 3 3 3 8 7.71 Bacter…
## 7 ASV_14… 3 3 3 3 8 7.71 Bacter…
## 8 ASV_23… 3 3 3 3 8 7.67 Bacter…
## 9 ASV_22… 3 3 3 3 8 7.70 Bacter…
## 10 ASV_218 3 3 3 3 1 0.955 Bacter…
## 11 ASV_14… 3 3 3 3 1 0.944 Bacter…
## # ℹ 6 more variables: Phylum <chr>, Class <chr>, Order <chr>, Family <chr>,
## # Genus <chr>, Species <chr>
## #
## # Edge Data: 38 × 5
## from to weight correlation corr_direction
## <int> <int> <dbl> <dbl> <chr>
## 1 1 2 0.982 0.982 Positive
## 2 1 3 0.985 0.985 Positive
## 3 2 3 0.986 0.986 Positive
## # ℹ 35 more rows
##
## $`4`
## # A tbl_graph: 11 nodes and 33 edges
## #
## # An undirected simple graph with 1 component
## #
## # Node Data: 11 × 14 (active)
## name modularity modularity2 modularity3 Modularity Degree Strength Kingdom
## <chr> <fct> <ord> <chr> <ord> <dbl> <dbl> <chr>
## 1 ASV_459 4 4 4 4 8 7.87 Bacter…
## 2 ASV_533 4 4 4 4 8 7.85 Bacter…
## 3 ASV_10… 4 4 4 4 8 7.87 Bacter…
## 4 ASV_13… 4 4 4 4 8 7.81 Bacter…
## 5 ASV_23… 4 4 4 4 8 7.87 Bacter…
## 6 ASV_24… 4 4 4 4 7 6.88 Bacter…
## 7 ASV_22… 4 4 4 4 7 6.81 Bacter…
## 8 ASV_29… 4 4 4 4 6 5.77 Bacter…
## 9 ASV_29… 4 4 4 4 4 3.79 Bacter…
## 10 ASV_746 4 4 4 4 1 0.945 Bacter…
## 11 ASV_19… 4 4 4 4 1 0.953 Bacter…
## # ℹ 6 more variables: Phylum <chr>, Class <chr>, Order <chr>, Family <chr>,
## # Genus <chr>, Species <chr>
## #
## # Edge Data: 33 × 5
## from to weight correlation corr_direction
## <int> <int> <dbl> <dbl> <chr>
## 1 1 2 0.997 0.997 Positive
## 2 1 3 1.000 1.000 Positive
## 3 2 3 0.998 0.998 Positive
## # ℹ 30 more rows
##
## $`6`
## # A tbl_graph: 11 nodes and 24 edges
## #
## # An undirected simple graph with 1 component
## #
## # Node Data: 11 × 14 (active)
## name modularity modularity2 modularity3 Modularity Degree Strength Kingdom
## <chr> <fct> <ord> <chr> <ord> <dbl> <dbl> <chr>
## 1 ASV_116 6 6 6 6 8 7.67 Bacter…
## 2 ASV_661 6 6 6 6 8 7.71 Bacter…
## 3 ASV_25… 6 6 6 6 6 5.79 Bacter…
## 4 ASV_975 6 6 6 6 5 4.78 Bacter…
## 5 ASV_10… 6 6 6 6 5 4.77 Bacter…
## 6 ASV_20… 6 6 6 6 5 4.79 Bacter…
## 7 ASV_27… 6 6 6 6 4 3.84 Bacter…
## 8 ASV_94 6 6 6 6 3 2.84 Bacter…
## 9 ASV_20… 6 6 6 6 2 1.92 Bacter…
## 10 ASV_442 6 6 6 6 1 0.946 Bacter…
## 11 ASV_408 6 6 6 6 1 0.959 Bacter…
## # ℹ 6 more variables: Phylum <chr>, Class <chr>, Order <chr>, Family <chr>,
## # Genus <chr>, Species <chr>
## #
## # Edge Data: 24 × 5
## from to weight correlation corr_direction
## <int> <int> <dbl> <dbl> <chr>
## 1 1 2 0.974 0.974 Positive
## 2 1 3 0.966 0.966 Positive
## 3 2 3 0.979 0.979 Positive
## # ℹ 21 more rows
##
## $`25`
## # A tbl_graph: 8 nodes and 22 edges
## #
## # An undirected simple graph with 1 component
## #
## # Node Data: 8 × 14 (active)
## name modularity modularity2 modularity3 Modularity Degree Strength Kingdom
## <chr> <fct> <ord> <chr> <ord> <dbl> <dbl> <chr>
## 1 ASV_1505 25 25 25 25 7 6.66 Bacter…
## 2 ASV_415 25 25 25 25 6 5.78 Bacter…
## 3 ASV_517 25 25 25 25 6 5.84 Bacter…
## 4 ASV_842 25 25 25 25 6 5.80 Bacter…
## 5 ASV_1719 25 25 25 25 6 5.85 Bacter…
## 6 ASV_2286 25 25 25 25 6 5.81 Bacter…
## 7 ASV_2637 25 25 25 25 5 4.78 Bacter…
## 8 ASV_1474 25 25 25 25 2 1.90 Bacter…
## # ℹ 6 more variables: Phylum <chr>, Class <chr>, Order <chr>, Family <chr>,
## # Genus <chr>, Species <chr>
## #
## # Edge Data: 22 × 5
## from to weight correlation corr_direction
## <int> <int> <dbl> <dbl> <chr>
## 1 1 2 0.947 0.947 Positive
## 2 1 3 0.951 0.951 Positive
## 3 2 3 0.970 0.970 Positive
## # ℹ 19 more rows
##
## $`7`
## # A tbl_graph: 6 nodes and 5 edges
## #
## # An unrooted tree
## #
## # Node Data: 6 × 14 (active)
## name modularity modularity2 modularity3 Modularity Degree Strength Kingdom
## <chr> <fct> <ord> <chr> <ord> <dbl> <dbl> <chr>
## 1 ASV_1896 7 7 7 7 3 2.87 Bacter…
## 2 ASV_454 7 7 7 7 2 1.89 Bacter…
## 3 ASV_1090 7 7 7 7 2 1.89 Bacter…
## 4 ASV_231 7 7 7 7 1 0.968 Bacter…
## 5 ASV_1800 7 7 7 7 1 0.943 Bacter…
## 6 ASV_2038 7 7 7 7 1 0.956 Bacter…
## # ℹ 6 more variables: Phylum <chr>, Class <chr>, Order <chr>, Family <chr>,
## # Genus <chr>, Species <chr>
## #
## # Edge Data: 5 × 5
## from to weight correlation corr_direction
## <int> <int> <dbl> <dbl> <chr>
## 1 1 2 0.945 0.945 Positive
## 2 2 3 0.944 0.944 Positive
## 3 1 4 0.968 0.968 Positive
## # ℹ 2 more rows
##
## $`12`
## # A tbl_graph: 5 nodes and 5 edges
## #
## # An undirected simple graph with 1 component
## #
## # Node Data: 5 × 14 (active)
## name modularity modularity2 modularity3 Modularity Degree Strength Kingdom
## <chr> <fct> <ord> <chr> <ord> <dbl> <dbl> <chr>
## 1 ASV_1148 12 12 12 12 4 3.85 Bacter…
## 2 ASV_1104 12 12 12 12 2 1.92 Bacter…
## 3 ASV_1854 12 12 12 12 2 1.95 Bacter…
## 4 ASV_115 12 12 12 12 1 0.955 Bacter…
## 5 ASV_2484 12 12 12 12 1 0.948 Bacter…
## # ℹ 6 more variables: Phylum <chr>, Class <chr>, Order <chr>, Family <chr>,
## # Genus <chr>, Species <chr>
## #
## # Edge Data: 5 × 5
## from to weight correlation corr_direction
## <int> <int> <dbl> <dbl> <chr>
## 1 1 2 0.959 0.959 Positive
## 2 1 3 0.990 0.990 Positive
## 3 2 3 0.957 0.957 Positive
## # ℹ 2 more rows
##
## $`22`
## # A tbl_graph: 5 nodes and 7 edges
## #
## # An undirected simple graph with 1 component
## #
## # Node Data: 5 × 14 (active)
## name modularity modularity2 modularity3 Modularity Degree Strength Kingdom
## <chr> <fct> <ord> <chr> <ord> <dbl> <dbl> <chr>
## 1 ASV_1931 22 22 22 22 4 3.88 Bacter…
## 2 ASV_1320 22 22 22 22 3 2.89 Bacter…
## 3 ASV_1906 22 22 22 22 3 2.91 Bacter…
## 4 ASV_2704 22 22 22 22 3 2.91 Bacter…
## 5 ASV_1495 22 22 22 22 1 0.970 Bacter…
## # ℹ 6 more variables: Phylum <chr>, Class <chr>, Order <chr>, Family <chr>,
## # Genus <chr>, Species <chr>
## #
## # Edge Data: 7 × 5
## from to weight correlation corr_direction
## <int> <int> <dbl> <dbl> <chr>
## 1 1 2 0.971 0.971 Positive
## 2 1 3 0.969 0.969 Positive
## 3 2 3 0.959 0.959 Positive
## # ℹ 4 more rows
##
## $`10`
## # A tbl_graph: 4 nodes and 3 edges
## #
## # An unrooted tree
## #
## # Node Data: 4 × 14 (active)
## name modularity modularity2 modularity3 Modularity Degree Strength Kingdom
## <chr> <fct> <ord> <chr> <ord> <dbl> <dbl> <chr>
## 1 ASV_2059 10 10 10 10 2 1.89 Bacter…
## 2 ASV_1965 10 10 10 10 2 1.91 Bacter…
## 3 ASV_544 10 10 10 10 1 0.964 Bacter…
## 4 ASV_1607 10 10 10 10 1 0.946 Bacter…
## # ℹ 6 more variables: Phylum <chr>, Class <chr>, Order <chr>, Family <chr>,
## # Genus <chr>, Species <chr>
## #
## # Edge Data: 3 × 5
## from to weight correlation corr_direction
## <int> <int> <dbl> <dbl> <chr>
## 1 1 2 0.943 0.943 Positive
## 2 2 3 0.964 0.964 Positive
## 3 1 4 0.946 0.946 Positive
##
## $`11`
## # A tbl_graph: 4 nodes and 3 edges
## #
## # An unrooted tree
## #
## # Node Data: 4 × 14 (active)
## name modularity modularity2 modularity3 Modularity Degree Strength Kingdom
## <chr> <fct> <ord> <chr> <ord> <dbl> <dbl> <chr>
## 1 ASV_614 11 11 11 11 2 1.91 Bacter…
## 2 ASV_2916 11 11 11 11 2 1.93 Bacter…
## 3 ASV_65 11 11 11 11 1 0.943 Archaea
## 4 ASV_2168 11 11 11 11 1 0.965 Bacter…
## # ℹ 6 more variables: Phylum <chr>, Class <chr>, Order <chr>, Family <chr>,
## # Genus <chr>, Species <chr>
## #
## # Edge Data: 3 × 5
## from to weight correlation corr_direction
## <int> <int> <dbl> <dbl> <chr>
## 1 1 2 0.966 0.966 Positive
## 2 1 3 0.943 0.943 Positive
## 3 2 4 0.965 0.965 Positive
##
## $`15`
## # A tbl_graph: 4 nodes and 3 edges
## #
## # An unrooted tree
## #
## # Node Data: 4 × 14 (active)
## name modularity modularity2 modularity3 Modularity Degree Strength Kingdom
## <chr> <fct> <ord> <chr> <ord> <dbl> <dbl> <chr>
## 1 ASV_172 15 15 15 15 2 1.92 Bacter…
## 2 ASV_246 15 15 15 15 2 1.91 Bacter…
## 3 ASV_43 15 15 15 15 1 0.969 Bacter…
## 4 ASV_2211 15 15 15 15 1 0.955 Bacter…
## # ℹ 6 more variables: Phylum <chr>, Class <chr>, Order <chr>, Family <chr>,
## # Genus <chr>, Species <chr>
## #
## # Edge Data: 3 × 5
## from to weight correlation corr_direction
## <int> <int> <dbl> <dbl> <chr>
## 1 1 2 0.952 0.952 Positive
## 2 1 3 0.969 0.969 Positive
## 3 2 4 0.955 0.955 Positive
##
## $Others
## # A tbl_graph: 39 nodes and 34 edges
## #
## # An undirected simple graph with 14 components
## #
## # Node Data: 39 × 14 (active)
## name modularity modularity2 modularity3 Modularity Degree Strength Kingdom
## <chr> <fct> <ord> <chr> <ord> <dbl> <dbl> <chr>
## 1 ASV_316 28 Others Others Others 3 2.89 Bacter…
## 2 ASV_610 28 Others Others Others 3 2.94 Bacter…
## 3 ASV_11… 29 Others Others Others 3 2.94 Bacter…
## 4 ASV_18… 29 Others Others Others 3 2.95 Bacter…
## 5 ASV_11… 27 Others Others Others 3 2.91 Bacter…
## 6 ASV_18… 28 Others Others Others 3 2.91 Bacter…
## 7 ASV_20… 29 Others Others Others 3 2.89 Bacter…
## 8 ASV_24… 27 Others Others Others 3 2.89 Bacter…
## 9 ASV_27… 29 Others Others Others 3 2.95 Bacter…
## 10 ASV_28… 28 Others Others Others 3 2.90 Bacter…
## # ℹ 29 more rows
## # ℹ 6 more variables: Phylum <chr>, Class <chr>, Order <chr>, Family <chr>,
## # Genus <chr>, Species <chr>
## #
## # Edge Data: 34 × 5
## from to weight correlation corr_direction
## <int> <int> <dbl> <dbl> <chr>
## 1 1 2 0.971 0.971 Positive
## 2 3 4 0.987 0.987 Positive
## 3 1 6 0.958 0.958 Positive
## # ℹ 31 more rows
subgraph_info$sub_graph_select## NULL