cohesionclass: Calculate the cohesion of samples for each network

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

Calculate the cohesion of samples for each network

Description

The cohesion is a method for quantifying the connectivity of microbial communities <doi:10.1038/ismej.2017.91>. It is defined:

C_{j}^{pos} = \sum_{i=1}^{n} a_{i} \cdot \bar{r_{i}}_{|r>0}

C_{j}^{neg} = \sum_{i=1}^{n} a_{i} \cdot \bar{r_{i}}_{|r<0}

where C_{j}^{pos} is the positive cohesion, and C_{j}^{neg} is the negative cohesion. a_{i} is the relative abundance of species i in sample j. \bar{r_{i}}_{|r>0} denotes the mean weight (correlation coefficient, interaction strength) of all the edges (related with species i) with positive association.

Methods

Public methods

• cohesionclass$new()

• cohesionclass$cal_diff()

• cohesionclass$plot()

• cohesionclass$clone()

---

Method new()

Usage

cohesionclass$new(network_list)

Arguments

network_list

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

Returns

res_list, stored in the object. It includes two tables: res_feature and res_sample. In res_feature, the r_pos and r_neg columns mean the \bar{r_{i}}_{|r>0} and \bar{r_{i}}_{|r<0}. In res_sample, the c_pos and c_neg columns denote C_{j}^{pos} and C_{j}^{neg}.

Examples

t1 <- cohesionclass$new(soil_amp_network)

---

Method cal_diff()

Differential test.

Usage

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

Arguments

measure

default "c_pos"; "c_pos" or "c_neg" in the res_list$sample; "r_pos" or "r_neg" in the res_list$feature.

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 result.

Usage

cohesionclass$plot(measure = "c_pos", ...)

Arguments

measure

default "c_pos"; "c_pos" or "c_neg" in the res_list$sample; "r_pos" or "r_neg" in the res_list$feature.

...

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

cohesionclass$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

## ------------------------------------------------
## Method `cohesionclass$new`
## ------------------------------------------------

t1 <- cohesionclass$new(soil_amp_network)


## ------------------------------------------------
## Method `cohesionclass$cal_diff`
## ------------------------------------------------


t1$cal_diff(method = "wilcox")


## ------------------------------------------------
## Method `cohesionclass$plot`
## ------------------------------------------------


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

meconetcomp documentation built on June 23, 2024, 9:06 a.m.