Package: MetaNet 0.3.1

Chen Peng

MetaNet: Network Analysis for Omics Data

Comprehensive network analysis package. Calculate correlation network fastly, accelerate lots of analysis by parallel computing. Support for multi-omics data, search sub-nets fluently. Handle bigger data, more than 10,000 nodes in each omics. Offer various layout method for multi-omics network and some interfaces to other software ('Gephi', 'Cytoscape', 'ggplot2'), easy to visualize. Provide comprehensive topology indexes calculation, including ecological network stability.

Authors:Chen Peng [aut, cre]

MetaNet_0.3.1.tar.gz
MetaNet_0.3.1.zip(r-4.7)MetaNet_0.3.1.zip(r-4.6)MetaNet_0.3.1.zip(r-4.5)
MetaNet_0.3.1.tgz(r-4.6-any)MetaNet_0.3.1.tgz(r-4.5-any)
MetaNet_0.3.1.tar.gz(r-4.7-any)MetaNet_0.3.1.tar.gz(r-4.6-any)
MetaNet_0.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MetaNet/json (API)

# Install 'MetaNet' in R:

install.packages('MetaNet', repos = c('https://asa12138.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/asa12138/metanet/issues

Datasets:

arc_count - Edgelist
arc_taxonomy - Edgelist
co_net - MetaNet networks
co_net_rmt - MetaNet networks
co_net2 - MetaNet networks
metab - MetaNet networks abundance
metab_g - MetaNet networks metadata
micro - MetaNet networks abundance
micro_g - MetaNet networks metadata
multi1 - MetaNet networks
transc - MetaNet networks abundance
transc_g - MetaNet networks metadata

On CRAN:

dataimport network analysis omics software visualization

7.39 score 116 stars 53 scripts 760 downloads 111 exports 38 dependencies

Last updated from:5c7ddcea25. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	231
source / vignettes	OK	266
linux-release-x86_64	OK	214
macos-release-arm64	OK	128
macos-oldrel-arm64	OK	149
windows-devel	OK	161
windows-release	OK	143
windows-oldrel	OK	170
wasm-release	OK	166

Exports:%<>%%>%adjacency_similarity anno_edge anno_vertex as_arc as_circle_tree as_coors as_line as_multi_layer as_poly_sector as_polyarc as_polycircle as_polygon as.ggig as.metanet c_net_annotate c_net_build c_net_cal c_net_calculate c_net_compare c_net_difference c_net_ego c_net_filter c_net_from_edgelist c_net_highlight c_net_index c_net_intersect c_net_lay c_net_layout c_net_load c_net_module c_net_neighbors c_net_plot c_net_save c_net_set c_net_skeleton c_net_stability c_net_union c_net_update cal_sim check_tabs clean_igraph clean_multi_edge_metanet Cohesion combine_n_module compare_rand df2net_tree extract_sample_net fast_cor filter_n_module fit_power g_layout g_layout_backbone g_layout_circlepack g_layout_multi_layer g_layout_nice g_layout_poly_sector g_layout_polyarc g_layout_polycircle g_layout_polygon g_layout_stress g_layout_treemap get_big_lay_nice get_community get_e get_group_skeleton get_module get_module_eigen get_n get_v input_cytoscape input_gephi is_metanet links_stat module_detect module_eigen module_expression module_net multi_net_build nc net_par netD3plot olympic_rings_net p.adjust.table plot_corr_heatmap plot_e_type_bar plot_module_tree plot_multi_nets plot_net_degree rand_net rand_net_par read_corr rmt RMT_threshold robust_test robustness save_corr show_MetaNet_logo skeleton_plot smallworldness spatstat_layout summ_2col summary_module to_module_net transform_coors twocol_edgelist venn_net vulnerability zp_analyse zp_plot

Dependencies:cli cpp11 dplyr farver generics ggnewscale ggplot2 ggrepel glue gtable igraph isoband labeling lattice lifecycle magrittr Matrix pcutils pillar pkgconfig plyr purrr R6 RColorBrewer Rcpp reshape2 rlang S7 scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr

MetaNet: Network Analysis for Omics Data

Install | Vignette | Citation | Need helps?

Rendered fromMetaNet.Rmdusingknitr::rmarkdown

Last update: 2024-03-21
Started: 2023-06-25

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate Similarity Between Two Graphs via Adjacency Matrices	adjacency_similarity
Use dataframe to annotate edges of an igraph	anno_edge
Use data.frame to annotate vertexes of metanet	anno_node anno_vertex
Edgelist	arc_count
Edgelist	arc_taxonomy
Layout as a arc	as_arc
Layout as a circle_tree	as_circle_tree
Transfer to a coors object	as_coors
Layout as a line	as_line
Layout as a multi_layer	as_multi_layer
Layout as a multi_layer	as_poly_sector
Layout as a polyarc	as_polyarc
Layout as a polycircle	as_polycircle
Layout as a polygon	as_polygon
Transfer an igraph object to a ggig	as.ggig
Annotate a metanet	c_net_annotate
Construct a metanet from a corr object	c_net_build
Calculate correlation for one or two t(otutab), or distance for one t(otutab).	c_net_cal c_net_calculate
Compare Two Networks	c_net_compare
Difference two networks	c_net_difference
Extract ego-centric subnetwork with preserved class attributes	c_net_ego c_net_neighbors
Filter a network according to some attributes	c_net_filter
Construct a network from edge_list dataframe	c_net_from_edgelist
Highlight specific nodes in a network	c_net_highlight
Intersect two networks	c_net_intersect
Layout coordinates	c_net_lay c_net_layout
Load network file	c_net_load
Plot a metanet	c_net_plot
Save network file	c_net_save
Set basic attributes from totu table	c_net_set
Evaluate the stability of a network	c_net_stability robustness robust_test vulnerability
Union two networks	c_net_union
Update a metanet object or transform igraph object to metanet object	as.metanet c_net_update
Calculate similarity for one t(otutab)	cal_sim
Check tables and extract common samples	check_tabs
Clean a igraph object	clean_igraph
Clean multi edge metanet to plot	clean_multi_edge_metanet
MetaNet networks	co_net
MetaNet networks	co_net_rmt
MetaNet networks	co_net2
Cohesion calculation	Cohesion plot.cohesion
Transform a dataframe to a network edgelist.	df2net_tree
Extract each sample network from the whole network	extract_sample_net
Fast correlation calculation	fast_cor
Filter some modules as others	combine_n_module filter_n_module plot_module_tree
Fit power-law distribution for an igraph	fit_power
Layout with group	g_layout
Layout with group nicely	get_big_lay_nice g_layout_backbone g_layout_circlepack g_layout_nice g_layout_stress g_layout_treemap
Layout with group	g_layout_poly_sector
Layout with group as a polygon	g_layout_multi_layer g_layout_polyarc g_layout_polycircle g_layout_polygon
Get community	get_community
Get edge information	get_e
Get skeleton network according to a group	c_net_skeleton get_group_skeleton skeleton_plot
Get module	get_module
Get module_eigen	get_module_eigen
Get network information	get_n
Get vertex information	get_v
Input a cyjs file exported by Cytoscape	input_cytoscape
Input a graphml file exported by Gephi	input_gephi
Is this object a metanet object?	is.metanet is_metanet
Link summary of the network	links_stat
MetaNet networks abundance	metab
MetaNet networks metadata	metab_g
MetaNet networks abundance	micro
MetaNet networks metadata	micro_g
Detect the modules	c_net_module module_detect
Calculate the eigenvalue of each module and correlation of nodes and eigenvalue (node_eigen_cor).	module_eigen module_expression
Generate a n-modules network	module_net
Multi-omics network build	multi_net_build
MetaNet networks	multi1
Calculate natural_connectivity	nc
Calculate all topological indexes of a network	c_net_index net_par
plot use networkD3	netD3plot
Plot olympic rings using network	olympic_rings_net
p.adjust apply on a correlation table (matrix or data.frame)	p.adjust.table
Plot a correlation heatmap	plot_corr_heatmap
Plot e_type bar	plot_e_type_bar
Batch drawing multiple network diagrams	plot_multi_nets
Plot degree distribution of networks	plot_net_degree
Plot a ggig	plot.ggig
Plot a metanet	plot.metanet
Plot a metanet_compare	plot.metanet_compare
Plot a rmt_res	plot.rmt_res
Plot robust	plot.robust
Plot robustness	plot.robustness
Plot vulnerability	plot.vulnerability
Print method for 'cohesion' objects	print.cohesion
Print method for 'coors' objects	print.coors
Print method for 'corr' objects	print.corr
Print method for 'ggig' objects	print.ggig
Print method for 'metanet' objects	print.metanet
Print method for 'metanet_compare' objects	print.metanet_compare
Print method for 'robust' objects	print.robust
Print method for 'robustness' objects	print.robustness
Print method for 'vulnerability' objects	print.vulnerability
Degree distribution comparison with random network	rand_net
Net_pars of many random network	compare_rand rand_net_par
Read a corr object	read_corr
Get RMT threshold for a correlation matrix	rmt RMT_threshold
Save a corr object	save_corr
Show MetaNet logo	show_MetaNet_logo
Calculate small-world coefficient	smallworldness
Generate spatial layout using 'spatstat'	spatstat_layout
Summaries two columns information	summ_2col
Summary module index	summary_module
Summary method for 'corr' objects	summary.corr
Transformation a network to a module network	to_module_net
MetaNet networks abundance	transc
MetaNet networks metadata	transc_g
Transform the layout of a 'coors' object	transform_coors
Quick build a metanet from two columns table	twocol_edgelist
Venn network	venn_net
Zi-Pi calculate	zp_analyse zp_plot

Package: MetaNet 0.3.1

MetaNet: Network Analysis for Omics Data

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)