WRC15 根际微生物多样性分析

这是一个微生物群落多样性分析项目，包含α多样性、β多样性分析与可视化图表。

项目结构

bin/ 脚本文件
data/ 原始数据
analyses/ 分析结果
figures/ 图片结果

Name		Name	Last commit message	Last commit date
Latest commit History 7 Commits
report_files/libs		report_files/libs
.Rprofile		.Rprofile
.gitignore		.gitignore
2015_WestResearchCampus_Sampling_Rhizo.csv		2015_WestResearchCampus_Sampling_Rhizo.csv
BacterialIndicators_Bac.txt		BacterialIndicators_Bac.txt
BacterialIndicators_Plant.txt		BacterialIndicators_Plant.txt
BacterialIndicators_all.txt		BacterialIndicators_all.txt
BacterialIndicators_av_only.txt		BacterialIndicators_av_only.txt
BacterialIndicators_bulk_only.txt		BacterialIndicators_bulk_only.txt
BacterialIndicators_ec_only.txt		BacterialIndicators_ec_only.txt
BacterialIndicators_no_bulk.txt		BacterialIndicators_no_bulk.txt
BacterialIndicators_plant_only.txt		BacterialIndicators_plant_only.txt
DiversityFunctions.R		DiversityFunctions.R
IndicatorSpeciesTable.xlsx		IndicatorSpeciesTable.xlsx
LICENSE		LICENSE
MothurTools.R		MothurTools.R
PCoA_plot.pdf		PCoA_plot.pdf
R		R
README.md		README.md
Richness_boxplot.pdf		Richness_boxplot.pdf
Shannon_boxplot.pdf		Shannon_boxplot.pdf
Shannon_by_Treatment.pdf		Shannon_by_Treatment.pdf
TableS1_IndicatorSpeciesTable.csv		TableS1_IndicatorSpeciesTable.csv
WRC15_genus_withSummaries_denovo.batch		WRC15_genus_withSummaries_denovo.batch
WRC2015Rhizo.Rmd		WRC2015Rhizo.Rmd
WRC2015RhizoDec2018.Rmd		WRC2015RhizoDec2018.Rmd
WRC2015RhizoDec2018.md		WRC2015RhizoDec2018.md
actino_family_composition.csv		actino_family_composition.csv
alpha_diversity_results.csv		alpha_diversity_results.csv
alpha_diversity_with_Treatment.csv		alpha_diversity_with_Treatment.csv
alpha_family_composition.csv		alpha_family_composition.csv
bray_curtis_distance_matrix.txt		bray_curtis_distance_matrix.txt
class_composition.csv		class_composition.csv
family_composition.csv		family_composition.csv
grass.high.boxplot.jpg		grass.high.boxplot.jpg
grass.high.heat.good.jpg		grass.high.heat.good.jpg
grass.high.heat.good.pdf		grass.high.heat.good.pdf
grass.high.heat.good.tiff		grass.high.heat.good.tiff
grass.low.heat.good.jpg		grass.low.heat.good.jpg
ind.tax.class.heat.good.jpg		ind.tax.class.heat.good.jpg
ind.tax.g.heat.good.jpg		ind.tax.g.heat.good.jpg
order_stack.pdf		order_stack.pdf
otu_matrix.csv		otu_matrix.csv
otu_ratio_pH_separate.jpg		otu_ratio_pH_separate.jpg
otu_ratio_pH_separate.pdf		otu_ratio_pH_separate.pdf
otu_ratio_pH_separate.tiff		otu_ratio_pH_separate.tiff
phylum_stack.pdf		phylum_stack.pdf
pielou.jpg		pielou.jpg
readme.txt		readme.txt
renv.lock		renv.lock
report.qmd		report.qmd
shannon.jpg		shannon.jpg
shannon.pdf		shannon.pdf
shannon_otu.jpg		shannon_otu.jpg
shannon_pH.jpg		shannon_pH.jpg
shannon_pH_separate.jpg		shannon_pH_separate.jpg
shannon_pH_separate.pdf		shannon_pH_separate.pdf
shannon_pH_separate.tiff		shannon_pH_separate.tiff
soil_properties_means.csv		soil_properties_means.csv
venn_all.png		venn_all.png
venn_fertilized.png		venn_fertilized.png
venn_forb.png		venn_forb.png
venn_grass.png		venn_grass.png
venn_unfertilized.pdf		venn_unfertilized.pdf
venn_unfertilized.png		venn_unfertilized.png
wrc15rhizodenovo.17May2018.opti_mcc.unique_list.0.03.cons.taxonomy		wrc15rhizodenovo.17May2018.opti_mcc.unique_list.0.03.cons.taxonomy
wrc15rhizodenovo.17May2018.opti_mcc.unique_list.shared		wrc15rhizodenovo.17May2018.opti_mcc.unique_list.shared

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