8.11 EMP_network_plot

The EMP_network_plot module can visualize the results of network analysis in graphical form. This section can be referenced together with Section 6.12.

8.11.1 Visualization of note importance

Note：
Parametershow could show the net or node。

🏷️Example:

MAE |>
  EMP_assay_extract('taxonomy') |>
  EMP_collapse(estimate_group = 'Genus',collapse_by = 'row') |>
  EMP_diff_analysis(method='wilcox.test', estimate_group = 'Group') |>
  EMP_filter(feature_condition = pvalue<0.05) |>
  EMP_network_analysis(coldata_to_assay = c('BMI','PHQ9','GAD7')) |>
  EMP_network_plot(show='node')

8.11.2 Visualization of network

Note：
This module inherits the parameter usage from qgraph.

🏷️Example:

k1 <- MAE |>
  EMP_assay_extract('taxonomy') |>
  EMP_collapse(estimate_group = 'Genus',collapse_by = 'row') |>
  EMP_diff_analysis(method='wilcox.test', estimate_group = 'Group') |>
  EMP_filter(feature_condition = pvalue<0.05)

k2 <- MAE |>
  EMP_collapse(experiment = 'untarget_metabol',na_string=c('NA','null','','-'),
               estimate_group = 'MS2kegg',method = 'sum',collapse_by = 'row') |>
  EMP_diff_analysis(method='DESeq2', .formula = ~Group) |>
  EMP_filter(feature_condition = pvalue<0.05)

(k1 + k2 ) |> 
  EMP_network_analysis() |> 
  EMP_network_plot(show = 'net',layout = 'spring',
                   shape='diamond',
                   edge.labels=TRUE,edge.label.cex=0.4,
                   vsize = 5,threshold = 0,
                   node_info = c('Phylum','MS2class'),
                   legend.cex=0.3,label.cex = 1,label.prop = 0.9,font=2)

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