使用 R 中的plotly 进行 3D 绘图

Question

我有2个数据框：

df1

           SeqTech      NMDS1       NMDS2        NMDS3         C1           C2          C3
AM.AD.1     Sanger -1.2408789  0.39893503 -0.036690753 -1.0330785 -0.009904179 -0.06261568
AM.AD.2     Sanger -0.9050894  0.55943858 -0.121985899 -1.0330785 -0.009904179 -0.06261568
AM.F10.T1   Sanger -0.9059108  0.09466239 -0.033827792 -1.0330785 -0.009904179 -0.06261568
AM.F10.T2   Sanger -0.8511172  0.21396548 -0.061612450 -1.0330785 -0.009904179 -0.06261568
DA.AD.1     Sanger -1.1390353  0.05166118  0.306245704 -1.0330785 -0.009904179 -0.06261568
DA.AD.1T    Sanger -1.2072895  0.06963215  0.241758582 -1.0330785 -0.009904179 -0.06261568
DA.AD.2     Sanger -1.1279367 -0.18692443 -0.092967153 -1.0330785 -0.009904179 -0.06261568
DA.AD.3     Sanger -1.3517083 -0.03651835  0.008165075 -1.0330785 -0.009904179 -0.06261568
DA.AD.3T    Sanger -1.2616186 -0.06099534 -0.016942073 -1.0330785 -0.009904179 -0.06261568
DA.AD.4     Sanger -1.2700349  0.10824017  0.150317712 -1.0330785 -0.009904179 -0.06261568
TS1_V2     Pyro454  0.2094447 -0.53605610  0.154892961  0.2750404  0.002636827  0.01667041
TS10_V2    Pyro454  0.3966404 -0.10453275 -0.016794425  0.2750404  0.002636827  0.01667041
TS100_V2   Pyro454  0.2409404 -0.19935538 -0.095123709  0.2750404  0.002636827  0.01667041
TS101.2_V2 Pyro454  0.3576462  0.78659670 -0.393325760  0.2750404  0.002636827  0.01667041
TS103_V2   Pyro454  0.6018257 -0.19066765  0.017434390  0.2750404  0.002636827  0.01667041
TS104_V2   Pyro454  0.2554765 -0.33614221 -0.009296729  0.2750404  0.002636827  0.01667041
TS105_V2   Pyro454  0.2898261  0.74827877 -0.531568414  0.2750404  0.002636827  0.01667041
TS106_V2   Pyro454  0.3539052  0.17369739 -0.181935984  0.2750404  0.002636827  0.01667041
TS107_V2   Pyro454  0.0385423  0.10432457  0.465820636  0.2750404  0.002636827  0.01667041
TS109_V2   Pyro454  0.2525936 -0.33896215 -0.173134963  0.2750404  0.002636827  0.01667041

df2

 SeqTech         C1           C2          C3
1 Pyro454  0.2750404  0.002636827  0.01667041
2  Sanger -1.0330785 -0.009904179 -0.06261568

我用它来制作二维图，例如：

ggplot(df1, aes_string(x = "NMDS1", y = "NMDS2" )) +
    geom_vline(xintercept = 0, linetype="dashed", size = 0.25, color= "#999999") + 
    geom_hline(yintercept = 0, linetype="dashed", size = 0.25, color= "#999999") +
    # sites
    geom_point(size = 2, alpha=0.3, aes_string(color= "SeqTech")) + 
    #Centroids
    geom_point(data = df2, aes_string(x="C1", y="C2", color=df2[,1]), size = 1, alpha=0.7, shape=19 ) +
    # Lines
    geom_segment(data = df1, aes_string(xend = "C1", yend = "C2", colour=df1$SeqTech ), alpha=0.3, linetype= "dashed" )

它导致

所以如果我想用plotly制作类似的东西，但用2D生成3D图。我有一个制作 3D 的代码，但我不知道如何连接这些点并生成一个中心点。

plotly::plot_ly(
    x=df1[,2],
    y=df1[,3],
    z=df1[,4],
    type="scatter3d",
    mode="markers",
    marker=list(size=3, opacity = 0.7),
    color=df1[, "SeqTech"],
    hovertemplate = paste(df1[,"SeqTech"])) 

如何在plotly中添加类似于geom_segment的内容？

非常感谢 ！！！

dput的df1

           SeqTech      NMDS1       NMDS2        NMDS3         C1           C2          C3
AM.AD.1     Sanger -1.2408789  0.39893503 -0.036690753 -1.0330785 -0.009904179 -0.06261568
AM.AD.2     Sanger -0.9050894  0.55943858 -0.121985899 -1.0330785 -0.009904179 -0.06261568
AM.F10.T1   Sanger -0.9059108  0.09466239 -0.033827792 -1.0330785 -0.009904179 -0.06261568
AM.F10.T2   Sanger -0.8511172  0.21396548 -0.061612450 -1.0330785 -0.009904179 -0.06261568
DA.AD.1     Sanger -1.1390353  0.05166118  0.306245704 -1.0330785 -0.009904179 -0.06261568
DA.AD.1T    Sanger -1.2072895  0.06963215  0.241758582 -1.0330785 -0.009904179 -0.06261568
DA.AD.2     Sanger -1.1279367 -0.18692443 -0.092967153 -1.0330785 -0.009904179 -0.06261568
DA.AD.3     Sanger -1.3517083 -0.03651835  0.008165075 -1.0330785 -0.009904179 -0.06261568
DA.AD.3T    Sanger -1.2616186 -0.06099534 -0.016942073 -1.0330785 -0.009904179 -0.06261568
DA.AD.4     Sanger -1.2700349  0.10824017  0.150317712 -1.0330785 -0.009904179 -0.06261568
TS1_V2     Pyro454  0.2094447 -0.53605610  0.154892961  0.2750404  0.002636827  0.01667041
TS10_V2    Pyro454  0.3966404 -0.10453275 -0.016794425  0.2750404  0.002636827  0.01667041
TS100_V2   Pyro454  0.2409404 -0.19935538 -0.095123709  0.2750404  0.002636827  0.01667041
TS101.2_V2 Pyro454  0.3576462  0.78659670 -0.393325760  0.2750404  0.002636827  0.01667041
TS103_V2   Pyro454  0.6018257 -0.19066765  0.017434390  0.2750404  0.002636827  0.01667041
TS104_V2   Pyro454  0.2554765 -0.33614221 -0.009296729  0.2750404  0.002636827  0.01667041
TS105_V2   Pyro454  0.2898261  0.74827877 -0.531568414  0.2750404  0.002636827  0.01667041
TS106_V2   Pyro454  0.3539052  0.17369739 -0.181935984  0.2750404  0.002636827  0.01667041
TS107_V2   Pyro454  0.0385423  0.10432457  0.465820636  0.2750404  0.002636827  0.01667041
TS109_V2   Pyro454  0.2525936 -0.33896215 -0.173134963  0.2750404  0.002636827  0.01667041

Answer 1

您需要以某种格式准备数据以输入到绘图中，以便绘图知道哪个点是哪个点，以及哪个点应该用线连接。下面是实现它的一种方法。

library(plotly)
library(dplyr)

# create a data_frame with two record per Name/SeqTech
# This will be provided to plotly for line drawing later
plotly_data <- bind_rows(
  data %>% select(Name, SeqTech, x = NMDS1, y = NMDS2, z= NMDS3),
  data %>% select(Name, SeqTech, x = C1, y = C2, z= C3)) %>%
  # define the group variable which will be used by plotly for line drawing
  group_by(Name)

# Here is what the data look like
plotly_data %>% arrange(Name) %>% head(20)
#>          Name SeqTech          x            y            z
#> 1     AM.AD.1  Sanger -1.2408789  0.398935030 -0.036690753
#> 2     AM.AD.1  Sanger -1.0330785 -0.009904179 -0.062615680
#> 3     AM.AD.2  Sanger -0.9050894  0.559438580 -0.121985899
#> 4     AM.AD.2  Sanger -1.0330785 -0.009904179 -0.062615680
#> 5   AM.F10.T1  Sanger -0.9059108  0.094662390 -0.033827792
#> 6   AM.F10.T1  Sanger -1.0330785 -0.009904179 -0.062615680
#> 7   AM.F10.T2  Sanger -0.8511172  0.213965480 -0.061612450
#> 8   AM.F10.T2  Sanger -1.0330785 -0.009904179 -0.062615680
#> 9     DA.AD.1  Sanger -1.1390353  0.051661180  0.306245704
#> 10    DA.AD.1  Sanger -1.0330785 -0.009904179 -0.062615680
#> 11   DA.AD.1T  Sanger -1.2072895  0.069632150  0.241758582
#> 12   DA.AD.1T  Sanger -1.0330785 -0.009904179 -0.062615680
#> 13    DA.AD.2  Sanger -1.1279367 -0.186924430 -0.092967153
#> 14    DA.AD.2  Sanger -1.0330785 -0.009904179 -0.062615680
#> 15    DA.AD.3  Sanger -1.3517083 -0.036518350  0.008165075
#> 16    DA.AD.3  Sanger -1.0330785 -0.009904179 -0.062615680
#> 17   DA.AD.3T  Sanger -1.2616186 -0.060995340 -0.016942073
#> 18   DA.AD.3T  Sanger -1.0330785 -0.009904179 -0.062615680
#> 19    DA.AD.4  Sanger -1.2700349  0.108240170  0.150317712
#> 20    DA.AD.4  Sanger -1.0330785 -0.009904179 -0.062615680

^{由reprex 包于 2021 年 5 月 11 日创建(v2.0.0)}

使用上面的数据绘制代码

# And here is the code for line & scatter point drawing with plotly
plotly::plot_ly(data = plotly_data %>% group_by(Name),
  x= ~x,
  y= ~y,
  z= ~z,
  # as the group is defined in the data the name can be define by SeqTech
  name = ~SeqTech,
  type="scatter3d",
  mode="lines+markers",
  marker=list(size=3, opacity = 0.7),
  color= ~SeqTech,
  hovertemplate = ~SeqTech)