在R和ggplot中用基本数据集显示轮廓故障 [英] Trouble displaying contours in R and ggplot with basic dataset

问题描述

我试图将一些NMDS坐标绘制为x和y，并使用多样性度量（shannon）将其绘制为轮廓，但我不断收到以下错误，我不明白为什么...

（空（new））返回（data.frame（））中的错误：
缺少值，其中TRUE / FALSE需要

我的代码是：

<$ p $ （all_merge，aes（NMDS1，NMDS2，z = shannon），其中， ））
p + geom_contour（）

和我的数据集是：

  NMDS1 NMDS2 shannon 
 -0.287555952 -0.129887595 9.516558582 
 -0.314104852 -0.048655648 8.985087924 
 -0.214910534 -0.127167065 8.928241917 
 -0.341295065 -0.296282805 8.315476782 
 -0.470025718 0.083835083 8.494348157 
 -0.429386114 0.044064347 8.669813919 
 -0.427608469 0.124631936 8.15886319 
 -0.584412991 0.257278736 8.469688185 
 -0.436526047 -0.070633108 8.496878956 
 -0.584707076 0.120411579 8.319057817 
 0.183493022 0.445239412 5.611249955 
 0.172968855 0.583787121 5.728358304 
 -0.404838098 -0.0271276 8.679667562 
 -0.458718755 -0.05638174 8.714026645 
 0.458621093 -0.186746574 8.094002558 
 1.148457698 0.044192391 6.058046032 
 0.346825668 0.258443444 6.682765975 
 0.753149083 -0.393018506 7.622032803 
 1.331546069 -0.515095457 5.784195943 
 0.236285309 0.2553056 7.210095451 
 0.346995457 -0.816928807 7.198583726 
 0.137626646 0.129803823 7.663931393 
 0.340733689 -0.461201268 5.845269914 
 -0.675116235 -0.037255181 8.371975231 
 -0.656523041 -0.025798291 8.438133054 
 -0.578757804 -0.073169316 8.411583639 
 -0.602672875 0.015207904 8.137468395 
 0.413598703 0.320133927 5.91489704 
 0.891714173 1.032329752 3.612230592 
 0.378252162 0.054121091 7.903450498 
 0.401158365 0.009307957 8.1 64654685 
 -0.074266368 -0.512745143 8.956733268 
  

解决方案

geom_contour （ stat_contour ）不适用于不规则网格（请参阅 here ）。创建常规网格的一种方式是在包 akima 中使用插值函数 interp 。

  library（akima）
 library（reshape2）
 
＃将数据内插到常规网格
 d1< ;  -  with（all_merge，interp（x = NMDS1，y = NMDS2，z = shannon））
 
＃将d1中的z矩阵融合为ggplot的长格式
 d2 < -  melt （d1 $ z，na.rm = TRUE）
名称（d2）< -c（x，y，shannon）
 
＃将NMDS1和NMDS2从d1使用相应的索引d1 
 d2 $ NMDS1 < -  d1 $ x [d2 $ x] 
 d2 $ NMDS2 < -  d1 $ y [d2 $ y] 
 
 $ plot 
 ggplot（data = d2，aes（x = NMDS1，y = NMDS2，fill = shannon，z = shannon））+ 
 geom_tile（）+ 
 stat_contour（）
  

I am trying to plot some NMDS co-ordinates as x and y, and use a diversity measure (shannon)to plot as a contour but I keep getting the following error and I can't see why...

Error in if (empty(new)) return(data.frame()) : 
  missing value where TRUE/FALSE needed

My code is:

all_merge <-read.table("test.txt", header=TRUE)

 p <- ggplot(all_merge, aes(NMDS1, NMDS2, z = shannon))
 p + geom_contour()

and my dataset is:

NMDS1   NMDS2   shannon
-0.287555952    -0.129887595    9.516558582
-0.314104852    -0.048655648    8.985087924
-0.214910534    -0.127167065    8.928241917
-0.341295065    -0.296282805    8.315476782
-0.470025718    0.083835083 8.494348157
-0.429386114    0.044064347 8.669813919
-0.427608469    0.124631936 8.15886319
-0.584412991    0.257278736 8.469688185
-0.436526047    -0.070633108    8.496878956
-0.584707076    0.120411579 8.319057817
0.183493022 0.445239412 5.611249955
0.172968855 0.583787121 5.728358304
-0.404838098    -0.0271276  8.679667562
-0.458718755    -0.05638174 8.714026645
0.458621093 -0.186746574    8.094002558
1.148457698 0.044192391 6.058046032
0.346825668 0.258443444 6.682765975
0.753149083 -0.393018506    7.622032803
1.331546069 -0.515095457    5.784195943
0.236285309 0.2553056   7.210095451
0.346995457 -0.816928807    7.198583726
0.137626646 0.129803823 7.663931393
0.340733689 -0.461201268    5.845269914
-0.675116235    -0.037255181    8.371975231
-0.656523041    -0.025798291    8.438133054
-0.578757804    -0.073169316    8.411583639
-0.602672875    0.015207904 8.137468395
0.413598703 0.320133927 5.91489704
0.891714173 1.032329752 3.612230592
0.378252162 0.054121091 7.903450498
0.401158365 0.009307957 8.164654685
-0.074266368    -0.512745143    8.956733268

解决方案

geom_contour (stat_contour) does not work on irregular grids (see here). One way to create a regular grid is to use the interpolation function interp in package akima.

library(akima)
library(reshape2)

# interpolate data to regular grid
d1 <- with(all_merge, interp(x = NMDS1, y = NMDS2, z = shannon))

# melt the z matrix in d1 to long format for ggplot
d2 <- melt(d1$z, na.rm = TRUE)
names(d2) <- c("x", "y", "shannon")

# add NMDS1 and NMDS2 from d1 using the corresponding index in d2
d2$NMDS1 <- d1$x[d2$x]
d2$NMDS2 <- d1$y[d2$y]

# plot
ggplot(data = d2, aes(x = NMDS1, y = NMDS2, fill = shannon, z = shannon)) +
  geom_tile() +
  stat_contour()

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