edge_node_distance: Perform the distance distribution of paired nodes in edges...

In meconetcomp: Compare Microbial Networks of 'trans_network' Class of 'microeco' Package

Perform the distance distribution of paired nodes in edges across networks.

Description

This class is a wrapper for a series of analysis on the distance values of paired nodes in edges across networks, including distance matrix conversion, the differential test and the visualization.

Methods

Public methods

• edge_node_distance$new()

• edge_node_distance$cal_diff()

• edge_node_distance$plot()

• edge_node_distance$clone()

---

Method new()

Usage

edge_node_distance$new(
  network_list,
  dis_matrix = NULL,
  label = "+",
  with_module = FALSE,
  module_thres = 2
)

Arguments

network_list

a list with multiple networks; all the networks should be trans_network object created from trans_network class of microeco package.

dis_matrix

default NULL; the distance matrix of nodes, used for the value extraction; must be a symmetrical matrix with both colnames and rownames (i.e. feature names).

label

default "+"; "+" or "-" or c("+", "-"); the edge label used for the selection of edges.

with_module

default FALSE; whether show the module classification of nodes in the result.

module_thres

default 2; the threshold of the nodes number of modules remained when with_module = TRUE.

Returns

data_table, stored in the object

Examples

\donttest{
data(soil_amp_network)
data(soil_amp)
# filter useless features to speed up the calculation
node_names <- unique(unlist(lapply(soil_amp_network, function(x){colnames(x$data_abund)})))
filter_soil_amp <- microeco::clone(soil_amp)
filter_soil_amp$otu_table <- filter_soil_amp$otu_table[node_names, ]
filter_soil_amp$tidy_dataset()
# obtain phylogenetic distance matrix
phylogenetic_distance <- as.matrix(cophenetic(filter_soil_amp$phylo_tree))
# choose the positive labels
t1 <- edge_node_distance$new(network_list = soil_amp_network, 
	 dis_matrix = phylogenetic_distance, label = "+")
}

---

Method cal_diff()

Differential test across networks.

Usage

edge_node_distance$cal_diff(
  method = c("anova", "KW", "KW_dunn", "wilcox", "t.test")[1],
  ...
)

Arguments

method

default "anova"; see the following available options:

'anova'

Duncan's multiple range test for anova

'KW'

KW: Kruskal-Wallis Rank Sum Test for all groups (>= 2)

'KW_dunn'

Dunn's Kruskal-Wallis Multiple Comparisons, see dunnTest function in FSA package

'wilcox'

Wilcoxon Rank Sum and Signed Rank Tests for all paired groups

't.test'

Student's t-Test for all paired groups

...

parameters passed to cal_diff function of trans_alpha class of microeco package.

Returns

res_diff in object. See the Return of cal_diff function in trans_alpha class of microeco package.

Examples

\donttest{
t1$cal_diff(method = "wilcox")
}

---

Method plot()

Plot the distance.

Usage

edge_node_distance$plot(...)

Arguments

...

parameters pass to plot_alpha function of trans_alpha class of microeco package.

Returns

ggplot.

Examples

\donttest{
t1$plot(boxplot_add = "none", add_sig = TRUE)
}

---

Method clone()

The objects of this class are cloneable with this method.

Usage

edge_node_distance$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

## ------------------------------------------------
## Method `edge_node_distance$new`
## ------------------------------------------------


data(soil_amp_network)
data(soil_amp)
# filter useless features to speed up the calculation
node_names <- unique(unlist(lapply(soil_amp_network, function(x){colnames(x$data_abund)})))
filter_soil_amp <- microeco::clone(soil_amp)
filter_soil_amp$otu_table <- filter_soil_amp$otu_table[node_names, ]
filter_soil_amp$tidy_dataset()
# obtain phylogenetic distance matrix
phylogenetic_distance <- as.matrix(cophenetic(filter_soil_amp$phylo_tree))
# choose the positive labels
t1 <- edge_node_distance$new(network_list = soil_amp_network, 
	 dis_matrix = phylogenetic_distance, label = "+")


## ------------------------------------------------
## Method `edge_node_distance$cal_diff`
## ------------------------------------------------


t1$cal_diff(method = "wilcox")


## ------------------------------------------------
## Method `edge_node_distance$plot`
## ------------------------------------------------


t1$plot(boxplot_add = "none", add_sig = TRUE)

meconetcomp documentation built on Nov. 18, 2023, 5:06 p.m.