├── .gitignore ├── LICENSE ├── README.md ├── data ├── bray_curtis_otu_table_css.txt ├── design.txt ├── otu_table.txt ├── otu_table_tax_L2.txt ├── otu_table_tax_L3.txt ├── otu_table_tax_L4.txt ├── otu_table_tax_L5.txt ├── otu_table_tax_L6.txt └── rep_seqs_tax.txt ├── fig1 ├── Illustrator Tutorial Floral, Swirl, Ornaments, Butterfly.mp4 ├── beta_pcoa_day_bray_curtis3.pdf ├── beta_pcoa_day_bray_curtis_default.pdf ├── beta_pcoa_day_bray_curtis_rainbow.pdf └── pcoa.r ├── fig2 ├── 2a.correlation_corrplot.R ├── 2e.diversity_final_distance_mean.r ├── corplot_pie_legend_time.pdf ├── corplot_pie_pearson_legend.pdf ├── e.beta_scatter_bray_curtis_mean6.pdf ├── e.boxplot.pdf ├── e.line.pdf └── ggcorrplot_pearson_A50Cp.pdf ├── fig3 ├── Top10phylum_ProClass.txt ├── tax_alluvium_phylumpro.pdf ├── tax_stack_phylumpro_sample.pdf ├── tax_stack_phylumpro_top9.pdf └── taxonomy_phylumpro.r └── fig4 ├── heatmap_groups.pdf ├── heatmap_samples.pdf ├── importance_class.txt ├── randomforest.R └── rf_imp_feature.pdf /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/README.md -------------------------------------------------------------------------------- /data/bray_curtis_otu_table_css.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/data/bray_curtis_otu_table_css.txt -------------------------------------------------------------------------------- /data/design.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/data/design.txt -------------------------------------------------------------------------------- /data/otu_table.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/data/otu_table.txt -------------------------------------------------------------------------------- /data/otu_table_tax_L2.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/data/otu_table_tax_L2.txt -------------------------------------------------------------------------------- /data/otu_table_tax_L3.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/data/otu_table_tax_L3.txt -------------------------------------------------------------------------------- /data/otu_table_tax_L4.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/data/otu_table_tax_L4.txt -------------------------------------------------------------------------------- /data/otu_table_tax_L5.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/data/otu_table_tax_L5.txt -------------------------------------------------------------------------------- /data/otu_table_tax_L6.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/data/otu_table_tax_L6.txt -------------------------------------------------------------------------------- /data/rep_seqs_tax.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/data/rep_seqs_tax.txt -------------------------------------------------------------------------------- /fig1/Illustrator Tutorial Floral, Swirl, Ornaments, Butterfly.mp4: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig1/Illustrator Tutorial Floral, Swirl, Ornaments, Butterfly.mp4 -------------------------------------------------------------------------------- /fig1/beta_pcoa_day_bray_curtis3.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig1/beta_pcoa_day_bray_curtis3.pdf -------------------------------------------------------------------------------- /fig1/beta_pcoa_day_bray_curtis_default.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig1/beta_pcoa_day_bray_curtis_default.pdf -------------------------------------------------------------------------------- /fig1/beta_pcoa_day_bray_curtis_rainbow.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig1/beta_pcoa_day_bray_curtis_rainbow.pdf -------------------------------------------------------------------------------- /fig1/pcoa.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig1/pcoa.r -------------------------------------------------------------------------------- /fig2/2a.correlation_corrplot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig2/2a.correlation_corrplot.R -------------------------------------------------------------------------------- /fig2/2e.diversity_final_distance_mean.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig2/2e.diversity_final_distance_mean.r -------------------------------------------------------------------------------- /fig2/corplot_pie_legend_time.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig2/corplot_pie_legend_time.pdf -------------------------------------------------------------------------------- /fig2/corplot_pie_pearson_legend.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig2/corplot_pie_pearson_legend.pdf -------------------------------------------------------------------------------- /fig2/e.beta_scatter_bray_curtis_mean6.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig2/e.beta_scatter_bray_curtis_mean6.pdf -------------------------------------------------------------------------------- /fig2/e.boxplot.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig2/e.boxplot.pdf -------------------------------------------------------------------------------- /fig2/e.line.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig2/e.line.pdf -------------------------------------------------------------------------------- /fig2/ggcorrplot_pearson_A50Cp.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig2/ggcorrplot_pearson_A50Cp.pdf -------------------------------------------------------------------------------- /fig3/Top10phylum_ProClass.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig3/Top10phylum_ProClass.txt -------------------------------------------------------------------------------- /fig3/tax_alluvium_phylumpro.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig3/tax_alluvium_phylumpro.pdf -------------------------------------------------------------------------------- /fig3/tax_stack_phylumpro_sample.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig3/tax_stack_phylumpro_sample.pdf -------------------------------------------------------------------------------- /fig3/tax_stack_phylumpro_top9.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig3/tax_stack_phylumpro_top9.pdf -------------------------------------------------------------------------------- /fig3/taxonomy_phylumpro.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig3/taxonomy_phylumpro.r -------------------------------------------------------------------------------- /fig4/heatmap_groups.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig4/heatmap_groups.pdf -------------------------------------------------------------------------------- /fig4/heatmap_samples.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig4/heatmap_samples.pdf -------------------------------------------------------------------------------- /fig4/importance_class.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig4/importance_class.txt -------------------------------------------------------------------------------- /fig4/randomforest.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig4/randomforest.R -------------------------------------------------------------------------------- /fig4/rf_imp_feature.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YongxinLiu/Zhang2018SCLS/HEAD/fig4/rf_imp_feature.pdf --------------------------------------------------------------------------------