数据点在直角坐标系平面上的分布图。A scatter plot (also called a scatter graph, scatter chart, scattergram, or scatter diagram) is a type of plot or mathematical diagram using Cartesian coordinates to display values for typically two variables for a set of data.
在宏基因组领域,散点图常用于展示样品组间的Beta多样性,常用的分析方法有主成分分析(PCA),主坐标轴分析(PCoA/MDS)和限制条件的主坐标轴分析(CPCoA/CCA/RDA)。
附图注原文:
(B) PCoA using the WUF metric indicates that the largest separation between microbial communities is spatial proximity to the root (PCo 1) and the second largest source of variation is soil type (PCo 2)
示例2. 以取材部位和基因型为条件的主坐标轴分析(CPCoA/CCA)
Zgadzaj, R., et.al., 2016 .PNAS
这篇文章分析了百脉根根瘤的微生物组成,同时在根瘤缺失突变体条件下发现根和根际微生物均有较大差异的变化。
(A) 采用CCA方法结合bray-curtis距离,分析以取样部分(compartment)条件下可显示各组最大差异投影平面;图顶部19.97% of variance (P<0.001)表示当前所展示的平面坐标系,可解释所有样品间总差异的19.97%的(另一种我的解读是当前条件对样品间总差异的贡献率为19.97%,即导致差异所占的权重),并且各组间存在显著差异(P<0.001);
附图注原文:
Fig. 2. (A) Constrained PCoA plot of Bray–Curtis distances between samples including only the WT constrained by compartment (19.97% of variance, P > 0.001; n = 94). (B) Constrained PCoA plot of Bray–Curtis distances constrained by genotype (9.82% of variance explained, P < 0.001; n = 164). Each point corresponds to a different sample colored by compartment, and each host genotype is represented by a different shape. The percentage of variation indicated in each axis corresponds to the fraction of the total variance explained by the projection.
Edwards, J., et al. (2015). “Structure, variation, and assembly of the root-associated microbiomes of rice.” Proceedings of the National Academy of Sciences 112(8): E911-E920.
Zgadzaj, R., Garrido-Oter, R., Jensen, D.B., Koprivova, A., Schulze-Lefert, P. and Radutoiu, S., 2016. Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities. Proceedings of the National Academy of Sciences, 113(49), pp.E7996-E8005.