SYMMF-net - SYnergistic Meta-Microbe Feature Network

SYMMF-net is a network analysis tool for Microbiome

Files for analysis

1. ERP004264_PD.table -- example file (Parkinson's disease)
2. NMF_analysis.R -- R script for NMF analysis
3. SYMMF_net_analysis.py -- Python script for SYMMF-net analysis

Running Script example

1. Running NMF_analysis.R script

$ Rscript NMF_analysis.R -m ERP004264_PD.table

2. Copy SYMMF_net_analysis.py to same folder as result of NMF_analsis.R

3. Running SYMMF_net_analysis.py script

$ python SYMMF_net_analysis.py -p 0.05

Development environment of R

R ver. = 3.4.0
required R packages
Bioconductor biobase
preprocessCore in Bioconductor
pheatmap
RColorBrewer
gplots
NMF
dendextend
dplyr
tidyr
reshape2
ggplot2
argparse

Output files after executing NMF_analysis.R

Clustering_purity_value.txt -- matrix of clustering purity results (m = 2 ~ 25)
raw_coefmat_[K#].txt -- coef matrix of each [K#]
raw_bmap_mat_[K#].txt -- basis matrix of each [K#]
group_coefmat_[K#].txt -- coef matrix of each [K#] group by each sample group
extracted_microb_feat_by_[K#].txt -- microbe list of each [K#]
disease_k_connect_by_[K#].tiff -- heatmap image of each group_coefmat_[K#].txt
basismatrix.pdf -- heatmap image of all basismap (m = 2 ~ 25)
coefmatrix.pdf -- heatmap image of all coefmap (m = 2 ~ 25)
micro_count_mat.txt -- input data matrix afeter and filtering
micro_count_mat_pre.txt -- input data matrix before filtering
microbe_list_original.txt -- microbe list of input data from original matrix
microbe_list_trimmed.txt -- microbe list of input data from trimmed matrix
sample_lable_list_trimmed.txt -- sample list of input data from trimmed matrix
MMF_microbe_list.txt -- microbe list and each contribution value from basismatrix

Development environment of Python

Python = 3.7.5
pandas = 0.25.3
numpy =  1.17.4
seaborn = 0.9.0
sklearn = 0.22
scipy = 1.3.2
matplotlib = 3.1.1
argparse = 1.1

Output files after executing SYMMF_net_analysis.py

mi_[Sample].data -- all of AUC value of each MMFs
kk_[Sample].data -- all of AUC value of each microbe
options_record.txt -- analysis option record
[Sample]_pairs_list.sif -- All microbe list from SYMMFs
AUC_value_list.txt -- All of AUC values all microbe and MMFs
MMF_high_AUC_and_list.data -- Sample specific MMF list and each AUC and highest micro AUC each MMF
microbe_AUC_calculation.xlsx -- AUC calculation result of each microbe
MMF_AUC_calculation.xlsx -- AUC calculation result of each MMF
SYMMF_summary_table.xlsx -- SYMMF information table
MMF_microbe_AUC_data_summary.xlsx -- all information of each MMF
NMF_result_summary.txt -- MMF information table
MMF_microbe_list_ordered.txt -- All microbe list of each MMF order by contribution value
SYMMF_feature_selected_microbe_list.txt -- microbe list from selected SYMMF of SYMMF-net

matrix of SYMMF

SYMMF_feature_bmap_selected.txt -- W_symmf matrix
SYMMF_feature_coef_selected.txt -- H_symmf matrix
SYMMF_feature_selected_microbe_count_mat.txt
cor_SYMMF_feature_bmap_selected.txt -- calculation result of correlation of each microbe from SYMMF_feature_bmap_selected.txt

Output for network generation

whole_network_cor[value]_p[value]_auc[value]_ECDF[value].sif -- cytoscape network file
whole_network_nodes_size_p[value]_auc[value]_ECDF[value].attrs -- network node info
whole_network_edges_cor[value]_p[value]_auc[value]_ECDF[value].attrs -- network edges info
whole_network_node_piechart_count_ratio_cor[value]_p[value]_auc[value]_ECDF[value].table -- network node info of pie-chart count
whole_network_node_piechart_contribution_ratio_cor[value]_p[value]_auc[value]_ECDF[value].table -- network node info of pie-chart contribution

R script for sub-analysis

SYMMF_feature_cor_gen.R -- Rscript for Pearson's correlation calculation
AUC_comparison_rscript.R -- Rscript for AUC comparison boxplot

Output Figures

NMF_microbe_AUC_comparison.tiff -- boxplot for AUC comparison between NMF and microbe
purification_comparison_plot.png -- Clustering purity comparison plot
all_SYMMF_MMF_scatter_plot.jpg -- scatter plot of all MMFs
SYMMF_MMF_scatter_plot_ECDF[value].jpg -- scatter plot of selected MMFs ECDF cut-off
MMF_AUC_save_kde_ECDF[value].png -- scatter plot of selected MMFs ECDF cut-off kde
MMF_AUC_save_hex_ECDF[value].png -- scatter plot of selected MMFs ECDF cut-off hex
SYMMFs_coefmap_mean_reord_save_ECDF[value].png -- heatmap of coefmap selected SYMMFs group by mean value
SYMMFs_coefmap_save_ECDF[value].png -- heatmap of coefmap selected SYMMFs
SYMMFs_basismap_reord_save_ECDF[value].png -- heatmap of basismap selected SYMMFs

Contributor

Keunwan Park (keunwan@kist.re.kr)
Young-Joon Ko (yjko@kist.re.kr)

Docker image

docker pull suppak/r340_symmf