network_analysis2: Conduct Network analysis

In LorMe: Lightening One-Code Resolving Microbial Ecology Solution

Conduct Network analysis

Description

A convenient and fast network analysis function, with output results suitable for cytoscape and gephi

Usage

network_analysis2(
  input,
  inputtype,
  n,
  threshold,
  method = "spearman",
  display = TRUE,
  input2,
  input2type
)

Arguments

input	Input dataframe with otu/gene/taxa in row and sample ID in column,at least 5 replicates(more than 8 replicates are recommened).
inputtype	Input dataframe type 1:dataframe with first column of OTUID and last column of taxonomy 2:dataframe with first column of OTUID/taxonomy 3:dataframe of all numeric
n	Only keep otu/gene/taxa appearing in n sample size
threshold	Threshold of correlation r value
method	A character string indicating which correlation coefficient is to be computed. One of "pearson" or "spearman"
display	If display a preview plot of network based on igraph. FALSE for the first attempt is recommended in case of too many vertices and edges.
input2	A second input data frame with otu/gene/taxa in row and sample ID in column. Default:NULL
input2type	The second input data frame type. Details the same as above. Default:NULL

Details

1. We had optimized the correlation algorithm to achieve a faster running speed. It takes less than 2 minute to calculate dataframe correlation and p value which more than 400 samples and 10000 OTUs for computer with dual Core i5 processor. However, too many vertices(>2000) or links(>10000) may slow the statistical process and visualization,so we recommend that in your first attempt,set display paramter as F to have a preview. Then you can adjust your n/threshold/method paramter to generate a suitable visualization network

2. We display a preview plot so as to adjusting your network. Generally a global figure (like we show in examples) with less than 1000 vertices and 5000 edges/links is recommended. Further more,we recommend you to output the statistics and adjacency table and use software like cytoscape or gephi for better visualization.

Value

One list contains a statistics table of network vertices/nodes and an adjacency table. One preview plot of network in the plot interface and an igraph object(named igraph1) in global environment.

Note

1. Replicates should be at least 5,more than 8 is recommend.

2. In case of too many edges/links or not a global network plot, you can stop the process immediately to provent wasting too much time.

Author(s)

Wang Ningqi [e-mail]

Examples

{
  ### Data preparation ###
  data(testotu)
  rownames(testotu) <- testotu[, 1]
  inputotu <- testotu[, -c(1, ncol(testotu))]
  head(inputotu)
  set.seed(999)
  ### One input network analysis ###
  network_result <- network_analysis2(
    inputotu,
    3,
    10,
    0.9,
    "spearman",
    TRUE
  )

  # Nodes information table
  network_nodes <- network_result$Nodes_info
  head(network_nodes)

  # Adjacency table
  network_adjacency <- network_result$Adjacency_column_table
  head(network_adjacency)

  # Complete adjacency matrix
  network_matrix <- network_result$Adjacency_matrix
  print(network_matrix[1:10, 1:10])

  # igraph object
  igraph_object <- network_result$Igraph_object
  network_stat(igraph_object)  # In case you want to see statistics again
  # or do other analysis based on igraph.

  ### Two inputs network analysis ###
  inputotu1 <- inputotu[1:456, ]
  inputotu2 <- inputotu[524:975, ]
  network_result <- network_analysis2(
    input = inputotu1,
    inputtype = 3,
    input2 = inputotu2,
    input2type = 3,
    n = 10,
    threshold = 0.85,
    method = "spearman",
    display = TRUE
  )

  #### Incorrect demonstration !! ###
  {
     network_result <- network_analysis2(inputotu, 3, 3, 0.8, "spearman", TRUE)
  }
  # Total edges/links: 10199
  # Total vertices: 826
  # Too many edges and not a global network

}

LorMe documentation built on Sept. 13, 2024, 9:07 a.m.