我正在用ggplot绘制dbRDA排序。
数据：
df1 <- structure(list(dbRDA1 = c(-0.277603544609864, -0.360978808436824,
-0.233134911000267, -0.310476800969782, -0.0906489101103515,
-0.145001415653946, -0.0332934057167847, -0.0275012617442552,
1.09301352917172, 1.06620520659396, -0.706049468959193, -0.322962763102308,
0.0621994470608108, 0.286233107477088), dbRDA2 = c(-0.0544365381093796,
-0.396097172755407, -0.179335397101395, -0.181894682898319, -0.0332360598060943,
-0.133901893994658, -0.231316948737708, -0.104267201073184, -0.446406664141594,
-0.324349265794935, 0.218701171555884, -0.0300275899654245, 0.595616680358468,
1.30095156246375), place = structure(c(2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("N", "O"), class = "factor"),
placecol = c("hollow", "hollow", "hollow", "hollow", "hollow",
"hollow", "hollow", "hollow", "non-hollow", "non-hollow",
"non-hollow", "non-hollow", "non-hollow", "non-hollow"),
treat = structure(c(2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L,
2L, 2L, 1L, 1L), .Label = c("10", "A"), class = "factor"),
OTU = c(1.358, 5.94, 1.119, 2.113, 1.12, 0.604, 1.525, 0.712,
1.841, 3.203, 2.512, 1.087, 1.087, 1.506)), .Names = c("dbRDA1",
"dbRDA2", "place", "placecol", "treat", "OTU"), row.names = c("60759",
"60773", "60774", "60775", "60776", "60777", "60778", "60779",
"60780", "60781", "60782", "60783", "60784", "60785"), class = "data.frame")
并绘制代码：
rda.plot <- ggplot(df1, aes(x=dbRDA1, y=dbRDA2, color=factor(treat),shape=factor(place))) +
geom_point(size=sqrt(df1$OTU)/sqrt(max(df1$OTU))*10,
aes(fill=factor(treat), alpha = as.factor(place)))+
geom_point(size=sqrt(df1$OTU)/sqrt(max(df1$OTU))*10) +
geom_text(aes(label=row.names(df1)),size=3, position = position_nudge(y = -0.1)) +
geom_hline(yintercept=0, linetype="dotted") +
geom_vline(xintercept=0, linetype="dotted") +
scale_shape_manual(values=c(21,24)) +
scale_alpha_manual(values=c(1,0)) +
scale_colour_manual(values = c("indianred3","lightskyblue4"))+
scale_fill_manual(values =alpha(c("indianred3","lightskyblue4")))+
coord_fixed()
rda.plot
如图所示，我有很多缩放比例和颜色代码，它们可以正常工作，但是（至少对我自己而言）令人困惑。它来自遵循一系列不同的准则（我想可以对其进行修剪）。
我想添加一个与环境矢量相对应的最后一层。
环境数据框：
vf_biplot <- structure(list(dbRDA1 = c(0.703799726303485, 0.108418920195407,
0.10268149348934, 0.393538121176574, -0.692749765298912), dbRDA2 = c(-0.507323360489587,
0.843331735032726, -0.549310027554416, -0.36248490838257, -0.291382798048848
), Envir = c("AA", "N",
"DOP", "Pm", "P")), .Names = c("dbRDA1", "dbRDA2",
"Envir"), row.names = c("AA", "N",
"DOP", "Pm", "P"), class = "data.frame")
我尝试添加图层（受stackoverflow启发）：
rda.plot + geom_segment(data = vf_biplot,
aes(x = 0, xend = dbRDA1, y = 0, yend = dbRDA2),
arrow = arrow(length = unit(0.25, "cm")), colour = "grey")+
geom_text(data = vf_biplot, aes(x = dbRDA1, y = dbRDA2, label = Envir),
size = 3)
我收到此错误：
Error in sort.list(y) : 'x' must be atomic for 'sort.list'
Have you called 'sort' on a list?
我用str()进行了检查，但vf_biplot或df1都不是列表（或包含列表）。