网站自己可以做么,顺德做网站,中国航空港建设总公司网站,海南在线新闻中心trans_beta class#xff1a;利用trans_beta类可以变换和绘制beta分集的距离矩阵。该类中涉及到beta多样性的分析主要包括排序、群距、聚类和方差分析。我们首先使用PCoA显示排序。 dataset$cal_betadiv()
The result is stored in object$beta_diversity ...t1 利用trans_beta类可以变换和绘制beta分集的距离矩阵。该类中涉及到beta多样性的分析主要包括排序、群距、聚类和方差分析。我们首先使用PCoA显示排序。 dataset$cal_betadiv()
The result is stored in object$beta_diversity ...t1 - trans_beta$new(dataset dataset, group Group, measure bray)t1$cal_ordination(ordination PCoA)
The ordination result is stored in object$res_ordination ...tmp - t1$res_ordination$scorest2 - trans_env$new(dataset dataset, add_data tmp[, 1:2])
Env data is stored in object$data_env ...t2$cal_diff(group Group, method anova)
The result is stored in object$res_diff ...
Warning message:
程辑包‘agricolae’是用R版本4.3.3 来建造的 #这里需要安装agricolae包直接install就行。t2
trans_env object:
Env table have 2 variables: PCo1,PCo2 p1 - t1$plot_ordination(plot_color Group, plot_shape Group, plot_type c(point, ellipse)) #然后我们绘制并比较群距。 t1$cal_group_distance() t1$plot_group_distance(distance_pair_stat TRUE) #这里应该会有差异比较的但是却没有。示例如下不知道有什么问题等到有需求我会解决这个问题。 #计算和绘制组之间的样本距离 t1$cal_group_distance(within_group FALSE) t1$plot_group_distance(distance_pair_stat TRUE) # 聚类图也是一种常用的方法。 t1$plot_clustering(group Group, replace_name c(Saline, Type)) #perMANOVA常用于组间距离的差异检验。 t1$cal_manova(cal_manova_all TRUE)
The result is stored in object$res_manova ...t1$res_manova
Permutation test for adonis under reduced model
Terms added sequentially (first to last)
Permutation: free
Number of permutations: 999adonis2(formula use_formula, data metadata, cal_manova_all TRUE)Df SumOfSqs R2 F Pr(F)
Group 2 6.1207 0.19553 10.573 0.001 ***
Residual 87 25.1822 0.80447
Total 89 31.3029 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
## manova表示每一对组 t1$cal_manova(cal_manova_paired TRUE)
The result is stored in object$res_manova ...t1$res_manova
Permutation test for adonis under reduced model
Terms added sequentially (first to last)
Permutation: free
Number of permutations: 999adonis2(formula use_formula, data metadata, cal_manova_paired TRUE)Df SumOfSqs R2 F Pr(F)
Group 2 6.1207 0.19553 10.573 0.001 ***
Residual 87 25.1822 0.80447
Total 89 31.3029 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
# manova用于指定组集:这里是“group Type”t1$cal_manova(cal_manova_set Group Type)
The result is stored in object$res_manova ...t1$res_manova
Permutation test for adonis under reduced model
Terms added sequentially (first to last)
Permutation: free
Number of permutations: 999adonis2(formula use_formula, data metadata, cal_manova_set Group Type)Df SumOfSqs R2 F Pr(F)
Group 2 6.1207 0.19553 10.573 0.001 ***
Residual 87 25.1822 0.80447
Total 89 31.3029 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
这个包的改动有些大以前的代码不能直接跑了。我发觉学习这个包还是要基于需求啊否则会很快忘掉。以前我使用vegan包分析ggplot2包做PCOA分析等把这个包分享完了我会再分享其它的R语言。
