fortify-isomap.md
In ggvegan: 'ggplot2' Plots for the 'vegan' Package

fortify works for isomap objects

Code
  fortify(dune_isomap)
Output
  # A tibble: 20 x 11
     label    dim1     dim2      dim3     dim4     dim5     dim6     dim7     dim8
     <chr>   <dbl>    <dbl>     <dbl>    <dbl>    <dbl>    <dbl>    <dbl>    <dbl>
   1 1      0.0124 -0.326    -6.87e-2 -1.97e-1  5.45e-1 -1.51e-2  7.56e-2  1.15e-2
   2 2      0.187   0.00765  -3.39e-2  3.58e-3  7.69e-2  1.21e-2  2.81e-2 -4.22e-3
   3 3     -0.169  -0.0466   -6.29e-3  3.30e-2  6.34e-2  1.72e-3  5.15e-2 -2.09e-2
   4 4     -0.0455 -0.259    -7.26e-3 -9.01e-3  1.19e-1  2.69e-2 -2.63e-1 -3.54e-4
   5 5      0.753   0.00594  -3.45e-1 -3.14e-1 -1.63e-1 -3.04e-2 -4.60e-3  1.68e-5
   6 6      0.737   0.0381   -3.00e-2 -3.52e-1 -1.43e-1  1.93e-1  1.63e-2  1.37e-3
   7 7      0.708   0.0464   -8.40e-2 -2.67e-1 -1.28e-1 -1.87e-1 -1.51e-2  1.34e-3
   8 8     -0.502  -0.0249    1.90e-2  7.13e-2 -5.51e-2 -1.89e-3  4.61e-2  2.63e-3
   9 9     -0.411  -0.330     4.09e-2  7.72e-2 -3.61e-2  1.44e-2 -1.45e-1 -2.04e-2
  10 10     0.493   0.0773   -5.08e-2  4.88e-4 -1.57e-2  2.32e-2  2.27e-2 -8.19e-4
  11 11     0.853   0.132     3.54e-1 -3.80e-2  5.14e-3 -2.36e-1 -1.94e-2 -4.75e-4
  12 12    -0.437  -0.506     6.62e-2  9.45e-2 -1.18e-1 -2.04e-2  2.14e-1 -3.72e-2
  13 13    -0.689  -0.607     1.01e-1  1.55e-1 -2.18e-1  9.45e-4 -3.50e-2  2.47e-2
  14 14    -1.44    0.432    -2.22e-2 -2.21e-2  1.89e-2  1.18e-3 -2.18e-2 -1.96e-1
  15 15    -1.26    0.344    -1.40e-2 -2.76e-3  2.91e-3  3.08e-4 -7.74e-4  2.49e-2
  16 16    -0.917   0.189     1.23e-5  3.03e-2 -2.25e-2 -5.26e-4  1.81e-2  1.12e-2
  17 17     1.01    0.0860   -5.51e-1  3.91e-1  2.10e-2  3.40e-2  6.25e-3 -7.93e-5
  18 18     0.912   0.135     4.51e-1 -7.75e-2  1.02e-2  1.86e-1  1.60e-2 -3.66e-4
  19 19     1.43    0.279     1.94e-1  4.24e-1  3.69e-2 -2.77e-3  2.66e-3  7.89e-4
  20 20    -1.24    0.327    -1.24e-2 -2.31e-4  1.42e-4 -9.08e-5  7.65e-3  2.02e-1
  # i 2 more variables: dim9 <dbl>, dim10 <dbl>

Code
  fortify(dune_isomap, what = "network")
Output
  # A tibble: 40 x 4
       xfrom    yfrom     xto      yto
       <dbl>    <dbl>   <dbl>    <dbl>
   1  0.187   0.00765  0.0124 -0.326  
   2 -0.169  -0.0466   0.0124 -0.326  
   3 -0.0455 -0.259    0.0124 -0.326  
   4 -0.169  -0.0466   0.187   0.00765
   5 -0.0455 -0.259    0.187   0.00765
   6  0.493   0.0773   0.187   0.00765
   7 -0.0455 -0.259   -0.169  -0.0466 
   8 -0.502  -0.0249  -0.169  -0.0466 
   9 -0.411  -0.330   -0.169  -0.0466 
  10 -0.437  -0.506   -0.169  -0.0466 
  # i 30 more rows

tidy works for isomap objects

Code
  tidy(dune_isomap)
Output
  # A tibble: 20 x 11
     label    dim1     dim2      dim3     dim4     dim5     dim6     dim7     dim8
     <chr>   <dbl>    <dbl>     <dbl>    <dbl>    <dbl>    <dbl>    <dbl>    <dbl>
   1 1      0.0124 -0.326    -6.87e-2 -1.97e-1  5.45e-1 -1.51e-2  7.56e-2  1.15e-2
   2 2      0.187   0.00765  -3.39e-2  3.58e-3  7.69e-2  1.21e-2  2.81e-2 -4.22e-3
   3 3     -0.169  -0.0466   -6.29e-3  3.30e-2  6.34e-2  1.72e-3  5.15e-2 -2.09e-2
   4 4     -0.0455 -0.259    -7.26e-3 -9.01e-3  1.19e-1  2.69e-2 -2.63e-1 -3.54e-4
   5 5      0.753   0.00594  -3.45e-1 -3.14e-1 -1.63e-1 -3.04e-2 -4.60e-3  1.68e-5
   6 6      0.737   0.0381   -3.00e-2 -3.52e-1 -1.43e-1  1.93e-1  1.63e-2  1.37e-3
   7 7      0.708   0.0464   -8.40e-2 -2.67e-1 -1.28e-1 -1.87e-1 -1.51e-2  1.34e-3
   8 8     -0.502  -0.0249    1.90e-2  7.13e-2 -5.51e-2 -1.89e-3  4.61e-2  2.63e-3
   9 9     -0.411  -0.330     4.09e-2  7.72e-2 -3.61e-2  1.44e-2 -1.45e-1 -2.04e-2
  10 10     0.493   0.0773   -5.08e-2  4.88e-4 -1.57e-2  2.32e-2  2.27e-2 -8.19e-4
  11 11     0.853   0.132     3.54e-1 -3.80e-2  5.14e-3 -2.36e-1 -1.94e-2 -4.75e-4
  12 12    -0.437  -0.506     6.62e-2  9.45e-2 -1.18e-1 -2.04e-2  2.14e-1 -3.72e-2
  13 13    -0.689  -0.607     1.01e-1  1.55e-1 -2.18e-1  9.45e-4 -3.50e-2  2.47e-2
  14 14    -1.44    0.432    -2.22e-2 -2.21e-2  1.89e-2  1.18e-3 -2.18e-2 -1.96e-1
  15 15    -1.26    0.344    -1.40e-2 -2.76e-3  2.91e-3  3.08e-4 -7.74e-4  2.49e-2
  16 16    -0.917   0.189     1.23e-5  3.03e-2 -2.25e-2 -5.26e-4  1.81e-2  1.12e-2
  17 17     1.01    0.0860   -5.51e-1  3.91e-1  2.10e-2  3.40e-2  6.25e-3 -7.93e-5
  18 18     0.912   0.135     4.51e-1 -7.75e-2  1.02e-2  1.86e-1  1.60e-2 -3.66e-4
  19 19     1.43    0.279     1.94e-1  4.24e-1  3.69e-2 -2.77e-3  2.66e-3  7.89e-4
  20 20    -1.24    0.327    -1.24e-2 -2.31e-4  1.42e-4 -9.08e-5  7.65e-3  2.02e-1
  # i 2 more variables: dim9 <dbl>, dim10 <dbl>

Code
  tidy(dune_isomap, what = "network")
Output
  # A tibble: 40 x 4
       xfrom    yfrom     xto      yto
       <dbl>    <dbl>   <dbl>    <dbl>
   1  0.187   0.00765  0.0124 -0.326  
   2 -0.169  -0.0466   0.0124 -0.326  
   3 -0.0455 -0.259    0.0124 -0.326  
   4 -0.169  -0.0466   0.187   0.00765
   5 -0.0455 -0.259    0.187   0.00765
   6  0.493   0.0773   0.187   0.00765
   7 -0.0455 -0.259   -0.169  -0.0466 
   8 -0.502  -0.0249  -0.169  -0.0466 
   9 -0.411  -0.330   -0.169  -0.0466 
  10 -0.437  -0.506   -0.169  -0.0466 
  # i 30 more rows