Sankey plot with plotly in R: how do I get the plot to skip over the NAs and not try to plot dead ends of some nodes?

huangapple
go评论96阅读模式
英文:

Sankey plot with plotly in R: how do I get the plot to skip over the NAs and not try to plot dead ends of some nodes?

问题

我已翻译代码和数据的主要部分，如下所示：

  1. #输出结构细节
  2. str(sank_test)
  4. 'data.frame':	168 obs. of  12 variables:
  5.  $ GobySpecies: int  1 1 1 1 1 1 1 2 2 2 ...
  6.  $ X2014      : chr  "An4" "Ate4" "Ate4" "Ate4" ...
  7.  $ X2015      : chr  "Ate5" "Ate5" "Ate5" "Ate5" ...
  8.  $ X2016      : chr  "An6" "Ate6" "Ate6" "Ate6" ...
  9.  $ X2018      : chr  "An8" "Ate8" "Av8" "Ac8" ...
  10.  $ X2020      : chr  "" "" "" "" ...
  11.  $ n          : int  10 29 12 29 12 1 7 25 18 4 ...
  12.  $ color      : chr  "red" "red" "red" "red" ...
  13.  $ color.1    : chr  "red" "red" "red" "red" ...
  14.  $ color.2    : chr  "red" "red" "red" "red" ...
  15.  $ color.3    : chr  "red" "red" "red" "red" ...
  16.  $ color.4    : chr  "red" "red" "red" "red" ...
  18. list.of.packages <- c("ggplot2","plotly","dplyr")
  19. new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
  20. if(length(new.packages)) install.packages(new.packages)
  21. #load specific packages of interest
  22. lapply(list.of.packages,library,character.only = TRUE)
  24. nodes_test <- data.frame(name = unique(c(as.character(sank_test$GobySpecies),
  25.                                     as.character(sank_test$X2014),
  26.                                     as.character(sank_test$X2015),
  27.                                     as.character(sank_test$X2016),
  28.                                     as.character(sank_test$X2018),
  29.                                     as.character(sank_test$X2020))))
  31. # create links_test dataframe
  32. links_test <- data.frame(source = match(sank_test$GobySpecies, nodes_test$name) - 1,
  33.                     target = match(sank_test$X2014, nodes_test$name) - 1,
  34.                     value = sank_test$n,
  35.                     stringsAsFactors = FALSE)
  37. links_test <- rbind(links_test,
  38.                data.frame(source = match(sank_test$X2014, nodes_test$name) - 1,
  39.                           target = match(sank_test$X2015, nodes_test$name) - 1,
  40.                           value = sank_test$n,
  41.                           stringsAsFactors = FALSE))
  42. links_test <- rbind(links_test,
  43.                data.frame(source = match(sank_test$X2015, nodes_test$name) - 1,
  44.                           target = match(sank_test$X2016, nodes_test$name) - 1,
  45.                           value = sank_test$n,
  46.                           stringsAsFactors = FALSE))
  48. links_test <- rbind(links_test,
  49.                data.frame(source = match(sank_test$X2016, nodes_test$name) - 1,
  50.                           target = match(sank_test$X2018, nodes_test$name) - 1,
  51.                           value = sank_test$n,
  52.                           stringsAsFactors = FALSE))
  54. links_test <- rbind(links_test,
  55.                data.frame(source = match(sank_test$X2018, nodes_test$name) - 1,
  56.                           target = match(sank_test$X2020, nodes_test$name) - 1,
  57.                           value = sank_test$n,
  58.                           stringsAsFactors = FALSE))
  61. plot_ly(
  62.   type = "sankey",
  63.   orientation = "h",
  64.   node = list(pad = 15,
  65.               thickness = 20,
  66.               line = list(color = "black", width = 0.5),
  67.               label = nodes_test$name,color="black"),
  68.   link = list(source = links_test$source,
  69.               target = links_test$target,
  70.               value = links_test$value,color = c(sank_test$color,sank_test$color.1,sank_test$color.2,sank_test$color.3,sank_test$color.4)),
  71.   textfont = list(size = 10),
  72.   width = 1000,
  73.   height = 480
  74. ) 
  76. # Code
  77. #make node colors same as link colors
  78. plot_ly(
  79.   type = "sankey",
  80.   orientation = "...

请注意，由于限制，我无法提供完整的代码和输出。如果您需要更多帮助或有其他问题，请告诉我。

英文:

I created a sankey plot with Plotly in R. I am happy with the color match up between the links and nodes (purposely only have the first column of nodes to be color matched up, and rest of the columns to be in black). However, some nodes are supposed to have dead ends for some links, which for some reason is not plotting correctly. Instead, my code is making a full loop and added a new node there (or shifted it over) for that loop (see bottom right corner with the purple, blue and yellow etc. looping). How do I get rid of that? You'll notice my dataframe has blanks in the columns where it should dead end. Later down in this question, I show that I figured out how to get rid of that looping node, but then I lost the follow up data (species 2 in orange), see below. Thanks in advance.

Sankey plot with plotly in R: how do I get the plot to skip over the NAs and not try to plot dead ends of some nodes?

Here is the head and tail of my data and then my code below. Each color corresponds to a specific GobySpecies for links and matches up with the node coloring that I added in my code in the plot_ly function:

  2. head(sank_test,100)
  3. GobySpecies X2014 X2015 X2016 X2018  X2020  n  color color.1 color.2 color.3
  4. 1            1   An4  Ate5   An6   An8        10    red     red     red     red
  5. 2            1  Ate4  Ate5  Ate6  Ate8        29    red     red     red     red
  6. 3            1  Ate4  Ate5  Ate6   Av8        12    red     red     red     red
  7. 4            1  Ate4  Ate5  Ate6   Ac8        29    red     red     red     red
  8. 5            1  Ate4  Ate5  Ate6   Al8        12    red     red     red     red
  9. 6            1  Ate4  Ate5   An6   An8         1    red     red     red     red
  10. 7            1  Ate4  Ate5  Ate6   An8         7    red     red     red     red
  11. 8            2   An4   An5   An6         An20 25 orange  orange  orange  orange
  12. 9            2   Am4   Am5   Am6         Ac20 18 orange  orange  orange  orange
  13. 10           2   Am4   An5   Am6       Aspp20  4 orange  orange  orange  orange
  14. 11           2   An4   Ac5   Ac6         Ac20  6 orange  orange  orange  orange
  15. 12           2   An4   An5   Ac6         Ac20  5 orange  orange  orange  orange
  16. 13           2   An4   An5   Ag6        Ase20  2 orange  orange  orange  orange
  17. 14           2   An4   An5   Ag6         Ac20 20 orange  orange  orange  orange
  18. 15           2   An4   An5   Al6         Al20  2 orange  orange  orange  orange
  19. 16           2   An4   An5   Al6         Ac20  4 orange  orange  orange  orange
  20. 17           2   An4   Av5   Av6         Ac20  6 orange  orange  orange  orange
  21. 18           2   An4   An5   An6         Ac20  8 orange  orange  orange  orange
  22. 19           3   Am4   Am5   Am6               6 yellow  yellow  yellow  yellow
  23. 20           3  Ato4  Ato5  Ato6               5 yellow  yellow  yellow  yellow
  24. 21           3 Aspp4 Aspp5 Aspp6              12 yellow  yellow  yellow  yellow
  25. 22           3   Am4   Am5   Ag6               7 yellow  yellow  yellow  yellow
  26. 23           3  Ato4   Am5  Ato6               3 yellow  yellow  yellow  yellow
  27. 24           3 Aspp4 Aspp5  Ato6               1 yellow  yellow  yellow  yellow
  28. 25           3  Ato4 Aspp5  Ato6               8 yellow  yellow  yellow  yellow
  29. 26           3  Ato4   An5   An6              29 yellow  yellow  yellow  yellow
  30. 27           3  Ato4   Ag5   Ag6              13 yellow  yellow  yellow  yellow
  31. 28           3  Ato4   Ar5   Ag6               3 yellow  yellow  yellow  yellow
  32. 29           3  Ato4  Ate5   Ag6               5 yellow  yellow  yellow  yellow
  33. 30           3  Ato4   Av5   Ag6               1 yellow  yellow  yellow  yellow
  34. 31           3  Ato4   Av5  Ato6               2 yellow  yellow  yellow  yellow
  35. 32           3  Ato4   Ac5  Ato6               5 yellow  yellow  yellow  yellow
  36. 33           4   Ac4   Ac5   Ac6   Ac8   Ac20  1  green   green   green   green
  37. 34           4   Al4   Al5   Al6   Al8   Al20  7  green   green   green   green
  38. 35           4   Ar4   Ar5   Ar6   Ar8   Ar20  2  green   green   green   green
  39. 36           4  Ate4  Ate5  Ate6  Ate8  Ate20  3  green   green   green   green
  40. 37           4   An4   An5   An6   An8   Ac20  5  green   green   green   green
  41. 38           4   Al4   Av5   Av6   Av8   Av20  9  green   green   green   green
  42. 39           4   Al4   Al5   Al6   Ag8   Ac20 10  green   green   green   green
  43. 40           4  Ate4  Ate5  Ato6  Ate8  Ate20  1  green   green   green   green
  44. 41           4 Aspp4   Ar5   Al6  Ate8 Aspp20  3  green   green   green   green
  45. 42           4   Ar4   Ar5   Av6   Ar8   Av20  1  green   green   green   green
  46. 43           4   Ac4   Al5   Al6   Ac8   Ac20  2  green   green   green   green
  47. 44           4   An4   An5   Al6   An8   Ac20  4  green   green   green   green
  48. 45           4  Ate4  Ate5   Al6  Ate8  Ate20  5  green   green   green   green
  49. 46           4   Al4   Al5   Al6   Al8   Ac20  2  green   green   green   green
  50. 47           4   An4   Al5   Al6   Ar8 Aspp20  6  green   green   green   green
  51. 48           4  Ate4   Av5   Av6  Ate8  Ase20  2  green   green   green   green
  52. 49           4   Al4   Al5   Al6   Ac8   Ac20  6  green   green   green   green
  53. 50           4   An4   Al5   Al6   Ac8   Ac20  2  green   green   green   green
  54. 51           4  Ate4   Ar5   Al6  Ate8   Av20 13  green   green   green   green
  55. 52           4  Ate4   Av5   Al6   Ac8   Av20  5  green   green   green   green
  56. 53           4   An4   Al5   Al6   Ac8 Aspp20  6  green   green   green   green
  57. 54           4  Ate4   Av5   Al6   Ac8 Aspp20  3  green   green   green   green
  58. 55           4  Ate4   Al5   Al6   Ac8 Aspp20  2  green   green   green   green
  59. 56           5   Ac4   Ac5   Ac6   Ac8   Ac20  5   cyan    cyan    cyan    cyan
  60. 57           5   An4   An5   An6   An8   An20 10   cyan    cyan    cyan    cyan
  61. 58           5  Ate4  Ate5  Ate6  Ate8  Ate20  1   cyan    cyan    cyan    cyan
  62. 59           5   Ag4   Ag5   Ag6   Ac8   Ac20  1   cyan    cyan    cyan    cyan
  63. 60           5   Ag4   Ag5   Ac6   Ac8   Ac20  2   cyan    cyan    cyan    cyan
  64. 61           5  Ate4  Ate5  Ate6  Ate8   Ac20  2   cyan    cyan    cyan    cyan
  65. 62           5  Ate4  Ate5   Al6  Ate8   Ac20  4   cyan    cyan    cyan    cyan
  66. 63           5   Al4   Al5   Al6   Ac8   Al20  1   cyan    cyan    cyan    cyan
  67. 64           5   Al4   Al5   Al6   Ac8   Ac20  1   cyan    cyan    cyan    cyan
  68. 65           5  Ate4   Am5   An6  Ate8   Ac20  4   cyan    cyan    cyan    cyan
  69. 66           5 Aspp4   Av5   Av6 Aspp8 Aspp20  1   cyan    cyan    cyan    cyan
  70. 67           5 Aspp4   Al5   Al6 Aspp8 Aspp20  2   cyan    cyan    cyan    cyan
  71. 68           5   Am4   Am5   Am6  Ate8   Ac20 32   cyan    cyan    cyan    cyan
  72. 69           5   An4   An5   An6   Ac8   An20 10   cyan    cyan    cyan    cyan
  73. 70           5   An4   An5   An6   Ac8   Ac20 11   cyan    cyan    cyan    cyan
  74. 71           5   An4   An5   Av6  Ase8  Ase20  1   cyan    cyan    cyan    cyan
  75. 72           5   An4   An5   Av6  Ase8   Ar20  1   cyan    cyan    cyan    cyan
  76. 73           5   An4   An5   Av6  Ase8   Ac20  3   cyan    cyan    cyan    cyan
  77. 74           5   An4   Ac5   Al6   Ac8   Ac20  2   cyan    cyan    cyan    cyan
  78. 75           5   An4   An5   Al6  Ate8   Ac20  1   cyan    cyan    cyan    cyan
  79. 76           5   An4   An5   Ac6  Ate8   Ac20  3   cyan    cyan    cyan    cyan
  80. 77           5   Am4   Am5   Av6 Aspp8   Ac20  1   cyan    cyan    cyan    cyan
  81. 78           5   Am4   Am5 Aspp6 Aspp8   Ac20  1   cyan    cyan    cyan    cyan
  82. 79           6   Am4   Am5   Am6              50   blue    blue    blue    blue
  83. 80           6   An4   An5   An6              14   blue    blue    blue    blue
  84. 81           6   Ag4   Ag5   Am6               4   blue    blue    blue    blue
  85. 82           6   Ac4   Am5   Am6               4   blue    blue    blue    blue
  86. 83           6 Aspp4   Am5   Am6               4   blue    blue    blue    blue
  87. color.4
  88. 1      red
  89. 2      red
  90. 3      red
  91. 4      red
  92. 5      red
  93. 6      red
  94. 7      red
  95. 8   orange
  96. 9   orange
  97. 10  orange
  98. 11  orange
  99. 12  orange
  100. 13  orange
  101. 14  orange
  102. 15  orange
  103. 16  orange
  104. 17  orange
  105. 18  orange
  106. 19  yellow
  107. 20  yellow
  108. 21  yellow
  109. 22  yellow
  110. 23  yellow
  111. 24  yellow
  112. 25  yellow
  113. 26  yellow
  114. 27  yellow
  115. 28  yellow
  116. 29  yellow
  117. 30  yellow
  118. 31  yellow
  119. 32  yellow
  120. 33   green
  121. 34   green
  122. 35   green
  123. 36   green
  124. 37   green
  125. 38   green
  126. 39   green
  127. 40   green
  128. 41   green
  129. 42   green
  130. 43   green
  131. 44   green
  132. 45   green
  133. 46   green
  134. 47   green
  135. 48   green
  136. 49   green
  137. 50   green
  138. 51   green
  139. 52   green
  140. 53   green
  141. 54   green
  142. 55   green
  143. 56    cyan
  144. 57    cyan
  145. 58    cyan
  146. 59    cyan
  147. 60    cyan
  148. 61    cyan
  149. 62    cyan
  150. 63    cyan
  151. 64    cyan
  152. 65    cyan
  153. 66    cyan
  154. 67    cyan
  155. 68    cyan
  156. 69    cyan
  157. 70    cyan
  158. 71    cyan
  159. 72    cyan
  160. 73    cyan
  161. 74    cyan
  162. 75    cyan
  163. 76    cyan
  164. 77    cyan
  165. 78    cyan
  166. 79    blue
  167. 80    blue
  168. 81    blue
  169. 82    blue
  170. 83    blue
  171. tail(sank_test,80)
  172. GobySpecies X2014 X2015 X2016 X2018  X2020  n  color color.1 color.2 color.3
  173. 89            6   Ag4   Av5   Av6               2   blue    blue    blue    blue
  174. 90            6   Ag4   Al5  Ato6               2   blue    blue    blue    blue
  175. 91            7   Ac4   Ac5   Ac6   Ac8   Ac20  8 purple  purple  purple  purple
  176. 92            7   An4   An5   An6   Ac8   An20 10 purple  purple  purple  purple
  177. 93            7   An4   An5   An6   Ac8   Ac20 42 purple  purple  purple  purple
  178. 94            7   Ac4   Ar5   Ac6  Ate8  Ate20  1 purple  purple  purple  purple
  179. 95            7   Ac4  Ato5   Ac6  Ate8  Ate20  1 purple  purple  purple  purple
  180. 96            7   Al4   Al5   Al6   Av8   Al20  2 purple  purple  purple  purple
  181. 97            7   Am4   Am5   Am6   Av8   Av20  2 purple  purple  purple  purple
  182. 98            7   An4   Al5   Av6   Av8   Av20  2 purple  purple  purple  purple
  183. 99            7   An4   Al5   Al6   Av8   Ac20  8 purple  purple  purple  purple
  184. 100           7 Aspp4   An5   Am6  Ate8 Aspp20  2 purple  purple  purple  purple
  185. 101           7   An4   Am5   Am6  Ate8   Al20  1 purple  purple  purple  purple
  186. 102           7   An4   Am5   Am6  Ate8   Av20  1 purple  purple  purple  purple
  187. 103           7   An4   Am5   Am6  Ate8 Aspp20  1 purple  purple  purple  purple
  188. 104           7   An4   An5   Av6   Av8   Ac20  1 purple  purple  purple  purple
  189. 105           7   An4   An5   Ac6  Ate8   Ac20  1 purple  purple  purple  purple
  190. 106           7   An4   Ag5   Ag6  Ate8   Ac20  3 purple  purple  purple  purple
  191. 107           7   An4   An5  Ate6  Ate8   Ac20  2 purple  purple  purple  purple
  192. 108           7   An4   An5   An6   Av8   Ac20  1 purple  purple  purple  purple
  193. 109           7   An4   An5   Am6  Ate8   Ac20  3 purple  purple  purple  purple
  194. 110           7   An4   Am5   Am6   Av8   Ac20  4 purple  purple  purple  purple
  195. 111           7   An4   Am5   Am6  Ate8   Ac20  4 purple  purple  purple  purple
  196. 112           8   Al4   Al5   Al6              10 violet  violet  violet  violet
  197. 113           8   Av4   Av5   Av6              12 violet  violet  violet  violet
  198. 114           8   Ag4   Al5   Al6               7 violet  violet  violet  violet
  199. 115           8  Ate4   Ar5   Al6              10 violet  violet  violet  violet
  200. 116           8 Aspp4   Ar5   Al6              23 violet  violet  violet  violet
  201. 117           8   Av4   Ar5   Av6               2 violet  violet  violet  violet
  202. 118           8   An4   Al5   Al6              22 violet  violet  violet  violet
  203. 119           8   An4   Al5   An6               1 violet  violet  violet  violet
  204. 120           8   Av4   Ar5   Al6              12 violet  violet  violet  violet
  205. 121           8   Av4   Al5   Al6               1 violet  violet  violet  violet
  206. 122           9   Al4   Al5   Al6   Al8   Al20  1   grey    grey    grey    grey
  207. 123           9   Am4   Am5   Am6   Am8   Am20  4   grey    grey    grey    grey
  208. 124           9   An4   An5   An6   An8   An20  3   grey    grey    grey    grey
  209. 125           9   Av4   Av5   Av6   Av8   Av20  3   grey    grey    grey    grey
  210. 126           9 Aspp4 Aspp5 Aspp6 Aspp8 Aspp20  5   grey    grey    grey    grey
  211. 127           9   An4   An5   An6   An8   Ac20 13   grey    grey    grey    grey
  212. 128           9   An4   An5   An6  Ase8  Ase20 16   grey    grey    grey    grey
  213. 129           9   Am4   Am5   Am6   Am8  Ase20  2   grey    grey    grey    grey
  214. 130           9  Ate4  Ate5  Ate6  Ate8   Ac20 10   grey    grey    grey    grey
  215. 131           9   Am4   Am5 Aspp6   Am8 Aspp20  6   grey    grey    grey    grey
  216. 132           9  Ato4  Ato5  Ato6   Av8  Ase20  3   grey    grey    grey    grey
  217. 133           9   Am4  Ato5  Ato6   Am8  Ase20  3   grey    grey    grey    grey
  218. 134           9   Ag4   Ag5   Ag6  Ate8   Ag20  3   grey    grey    grey    grey
  219. 135           9   Ag4   Ag5   Ag6   Al8   Al20  2   grey    grey    grey    grey
  220. 136           9   Ag4   Al5   Ag6   Al8   Al20  1   grey    grey    grey    grey
  221. 137           9   Ag4   Al5   Ag6   Am8   Al20  1   grey    grey    grey    grey
  222. 138           9   Am4   Av5  Ato6   Am8  Ase20  2   grey    grey    grey    grey
  223. 139           9 Aspp4  Ate5  Ate6  Ate8 Aspp20  1   grey    grey    grey    grey
  224. 140           9   Av4   Av5   Av6   Av8  Ase20  2   grey    grey    grey    grey
  225. 141           9   Ac4   Av5   Ac6   Ac8   Ac20  7   grey    grey    grey    grey
  226. 142           9   Al4   Al5   Ac6   Ac8   Ac20  1   grey    grey    grey    grey
  227. 143           9   An4 Aspp5   Ac6   Ac8   Ac20  4   grey    grey    grey    grey
  228. 144           9   An4   An5   An6   An8  Ase20  2   grey    grey    grey    grey
  229. 145           9 Aspp4 Aspp5   An6  Ase8  Ase20  2   grey    grey    grey    grey
  230. 146           9   Ac4 Aspp5   Ac6   Ac8   Ac20  2   grey    grey    grey    grey
  231. 147           9   Ac4  Ate5  Ato6   Av8 Aspp20  1   grey    grey    grey    grey
  232. 148          10   Ag4   Ag5   Ag6   Ag8        10  black   black   black   black
  233. 149          10   Al4   Al5   Al6   Al8         1  black   black   black   black
  234. 150          10   An4   An5   An6   An8         4  black   black   black   black
  235. 151          10   Al4   Ag5   Al6   Al8         1  black   black   black   black
  236. 152          10   Al4 Aspp5 Aspp6   Al8         1  black   black   black   black
  237. 153          10   Ag4   Ag5   Ac6   Ac8         1  black   black   black   black
  238. 154          10   Ag4   Ag5   Ag6   Ac8        20  black   black   black   black
  239. 155          10   Ag4   Ag5   Am6   Am8         2  black   black   black   black
  240. 156          10   Ag4   Ag5   Ag6   Am8         1  black   black   black   black
  241. 157          10   An4   Ag5   An6   An8         1  black   black   black   black
  242. 158          10   Ag4   Ag5   An6   An8         4  black   black   black   black
  243. 159          10   Ag4   Ag5   Ag6   Ar8         3  black   black   black   black
  244. 160          10  Ato4  Ato5  Ato6  Ase8         1  black   black   black   black
  245. 161          10  Ato4 Aspp5  Ato6  Ase8         1  black   black   black   black
  246. 162          10  Ato4   Ag5 Aspp6 Aspp8         1  black   black   black   black
  247. 163          10  Ate4   Ag5 Aspp6 Aspp8         5  black   black   black   black
  248. 164          10   Ag4   Ag5   Av6   Av8         1  black   black   black   black
  249. 165          10   Ag4   Ag5   Ag6   Av8         2  black   black   black   black
  250. 166          10   Ag4   Ag5   Ag6   An8        16  black   black   black   black
  251. 167          10   Ag4   Ag5   Ag6  Ase8        16  black   black   black   black
  252. 168          10   Ag4   Ag5   Ag6 Aspp8         8  black   black   black   black
  253. color.4
  254. 89     blue
  255. 90     blue
  256. 91   purple
  257. 92   purple
  258. 93   purple
  259. 94   purple
  260. 95   purple
  261. 96   purple
  262. 97   purple
  263. 98   purple
  264. 99   purple
  265. 100  purple
  266. 101  purple
  267. 102  purple
  268. 103  purple
  269. 104  purple
  270. 105  purple
  271. 106  purple
  272. 107  purple
  273. 108  purple
  274. 109  purple
  275. 110  purple
  276. 111  purple
  277. 112  violet
  278. 113  violet
  279. 114  violet
  280. 115  violet
  281. 116  violet
  282. 117  violet
  283. 118  violet
  284. 119  violet
  285. 120  violet
  286. 121  violet
  287. 122    grey
  288. 123    grey
  289. 124    grey
  290. 125    grey
  291. 126    grey
  292. 127    grey
  293. 128    grey
  294. 129    grey
  295. 130    grey
  296. 131    grey
  297. 132    grey
  298. 133    grey
  299. 134    grey
  300. 135    grey
  301. 136    grey
  302. 137    grey
  303. 138    grey
  304. 139    grey
  305. 140    grey
  306. 141    grey
  307. 142    grey
  308. 143    grey
  309. 144    grey
  310. 145    grey
  311. 146    grey
  312. 147    grey
  313. 148   black
  314. 149   black
  315. 150   black
  316. 151   black
  317. 152   black
  318. 153   black
  319. 154   black
  320. 155   black
  321. 156   black
  322. 157   black
  323. 158   black
  324. 159   black
  325. 160   black
  326. 161   black
  327. 162   black
  328. 163   black
  329. 164   black
  330. 165   black
  331. 166   black
  332. 167   black
  333. 168   black

Here is the code

  1. #spit out structure details
  2. str(sank_test)
  3. &#39;data.frame&#39;:	168 obs. of  12 variables:
  4. $ GobySpecies: int  1 1 1 1 1 1 1 2 2 2 ...
  5. $ X2014      : chr  &quot;An4&quot; &quot;Ate4&quot; &quot;Ate4&quot; &quot;Ate4&quot; ...
  6. $ X2015      : chr  &quot;Ate5&quot; &quot;Ate5&quot; &quot;Ate5&quot; &quot;Ate5&quot; ...
  7. $ X2016      : chr  &quot;An6&quot; &quot;Ate6&quot; &quot;Ate6&quot; &quot;Ate6&quot; ...
  8. $ X2018      : chr  &quot;An8&quot; &quot;Ate8&quot; &quot;Av8&quot; &quot;Ac8&quot; ...
  9. $ X2020      : chr  &quot;&quot; &quot;&quot; &quot;&quot; &quot;&quot; ...
  10. $ n          : int  10 29 12 29 12 1 7 25 18 4 ...
  11. $ color      : chr  &quot;red&quot; &quot;red&quot; &quot;red&quot; &quot;red&quot; ...
  12. $ color.1    : chr  &quot;red&quot; &quot;red&quot; &quot;red&quot; &quot;red&quot; ...
  13. $ color.2    : chr  &quot;red&quot; &quot;red&quot; &quot;red&quot; &quot;red&quot; ...
  14. $ color.3    : chr  &quot;red&quot; &quot;red&quot; &quot;red&quot; &quot;red&quot; ...
  15. $ color.4    : chr  &quot;red&quot; &quot;red&quot; &quot;red&quot; &quot;red&quot; ...
  16. list.of.packages &lt;- c(&quot;ggplot2&quot;,&quot;plotly&quot;,&quot;dplyr&quot;)
  17. new.packages &lt;- list.of.packages[!(list.of.packages %in% installed.packages()[,&quot;Package&quot;])]
  18. if(length(new.packages)) install.packages(new.packages)
  19. #load specific packages of interest
  20. lapply(list.of.packages,library,character.only = TRUE)
  21. nodes_test &lt;- data.frame(name = unique(c(as.character(sank_test$GobySpecies),
  22. as.character(sank_test$X2014),
  23. as.character(sank_test$X2015),
  24. as.character(sank_test$X2016),
  25. as.character(sank_test$X2018),
  26. as.character(sank_test$X2020))))
  27. # create links_test dataframe
  28. links_test &lt;- data.frame(source = match(sank_test$GobySpecies, nodes_test$name) - 1,
  29. target = match(sank_test$X2014, nodes_test$name) - 1,
  30. value = sank_test$n,
  31. stringsAsFactors = FALSE)
  32. links_test &lt;- rbind(links_test,
  33. data.frame(source = match(sank_test$X2014, nodes_test$name) - 1,
  34. target = match(sank_test$X2015, nodes_test$name) - 1,
  35. value = sank_test$n,
  36. stringsAsFactors = FALSE))
  37. links_test &lt;- rbind(links_test,
  38. data.frame(source = match(sank_test$X2015, nodes_test$name) - 1,
  39. target = match(sank_test$X2016, nodes_test$name) - 1,
  40. value = sank_test$n,
  41. stringsAsFactors = FALSE))
  42. links_test &lt;- rbind(links_test,
  43. data.frame(source = match(sank_test$X2016, nodes_test$name) - 1,
  44. target = match(sank_test$X2018, nodes_test$name) - 1,
  45. value = sank_test$n,
  46. stringsAsFactors = FALSE))
  47. links_test &lt;- rbind(links_test,
  48. data.frame(source = match(sank_test$X2018, nodes_test$name) - 1,
  49. target = match(sank_test$X2020, nodes_test$name) - 1,
  50. value = sank_test$n,
  51. stringsAsFactors = FALSE))
  52. plot_ly(
  53. type = &quot;sankey&quot;,
  54. orientation = &quot;h&quot;,
  55. node = list(pad = 15,
  56. thickness = 20,
  57. line = list(color = &quot;black&quot;, width = 0.5),
  58. label = nodes_test$name,color=&quot;black&quot;),
  59. link = list(source = links_test$source,
  60. target = links_test$target,
  61. value = links_test$value,color = c(sank_test$color,sank_test$color.1,sank_test$color.2,sank_test$color.3,sank_test$color.4)),
  62. textfont = list(size = 10),
  63. width = 1000,
  64. height = 480
  65. ) 
  66. # Code
  67. #make node colors same as link colors
  68. plot_ly(
  69. type = &quot;sankey&quot;,
  70. orientation = &quot;h&quot;,
  71. node = list(pad = 15,
  72. thickness = 20,
  73. line = list(color = &quot;black&quot;, width = 0.5),
  74. label = nodes_test$name,color=c(&quot;red&quot;,&quot;orange&quot;,&quot;yellow&quot;,&quot;green&quot;,&quot;cyan&quot;,&quot;blue&quot;,&quot;purple&quot;,&quot;violet&quot;,&quot;grey&quot;,&quot;black&quot;)),
  75. link = list(source = links_test$source,
  76. target = links_test$target,
  77. value = links_test$value,color = c(sank_test$color,sank_test$color.1,sank_test$color.2,sank_test$color.3,sank_test$color.4)),
  78. textfont = list(size = 10),
  79. width = 1000,
  80. height = 480
  81. )

I figured out how to get rid of the loop, but now one species (2, color=orange) is no longer showing anything in the last 'column to the right in the figure. Here is what I troubleshooted:when generating the node file, the code automatically generated a node for the blanks in certain cells. That node was a blank label in the node dataframe (here in nodes_test dataframe). So I removed the specific blank label (row 46) in the nodes dataframe and ran the rest as usual.

Sankey plot with plotly in R: how do I get the plot to skip over the NAs and not try to plot dead ends of some nodes?
Here is the nodes file initially so you can see the blank node that it created and then I have the code to remove it. Note, I also added a line of code that renamed the column to 'name':

  1. 1           G. aoyagii
  2. 2         G. axillaris
  3. 3        G. bilineatus
  4. 4           G. brochus
  5. 5     G. erythrospilus
  6. 6        G. fuscoruber
  7. 7           G. histrio
  8. 8     G. oculolineatus
  9. 9  G. quinquestrigatus
  10. 10        G. rivulatus
  11. 11       A. nasuta2014
  12. 12       A. tenuis2014
  13. 13    A. millepora2014
  14. 14   A. torresiana2014
  15. 15         A. spp.2014
  16. 16     A. cerealis2014
  17. 17      A. loripes2014
  18. 18      A. rosaria2014
  19. 19    A. gemmifera2014
  20. 20       A. valida2014
  21. 21       A. tenuis2015
  22. 22       A. nasuta2015
  23. 23    A. millepora2015
  24. 24     A. cerealis2015
  25. 25       A. valida2015
  26. 26   A. torresiana2015
  27. 27         A. spp.2015
  28. 28    A. gemmifera2015
  29. 29      A. rosaria2015
  30. 30      A. loripes2015
  31. 31       A. nasuta2016
  32. 32       A. tenuis2016
  33. 33    A. millepora2016
  34. 34     A. cerealis2016
  35. 35    A. gemmifera2016
  36. 36      A. loripes2016
  37. 37       A. valida2016
  38. 38   A. torresiana2016
  39. 39         A. spp.2016
  40. 40      A. rosaria2016
  41. 41       A. nasuta2018
  42. 42       A. tenuis2018
  43. 43       A. valida2018
  44. 44     A. cerealis2018
  45. 45      A. loripes2018
  46. 46                    
  47. 47      A. rosaria2018
  48. 48    A. gemmifera2018
  49. 49         A. spp.2018
  50. 50       A. selago2018
  51. 51    A. millepora2018
  52. 52       A. nasuta2020
  53. 53     A. cerealis2020
  54. 54         A. spp.2020
  55. 55       A. selago2020
  56. 56      A. loripes2020
  57. 57      A. rosaria2020
  58. 58       A. tenuis2020
  59. 59       A. valida2020
  60. 60    A. millepora2020
  61. 61    A. gemmifera2020

here is the code for removing that node

  1. #NOW WITH NA NODE REMOVED
  2. #remove node that is NA
  3. nodes_test = data.frame(nodes_test[-c(46),])
  4. #rename column
  5. colnames(nodes_test)[1]=&#39;name&#39;

答案1

得分: 0

我已经搞清楚了，所以我在这里发布，以防其他人有同样的问题。在生成节点文件时，代码会自动生成某些单元格中空白的节点。该节点是节点数据框中的一个空白标签（在这里是nodes_test数据框中的第46行）。因此，我删除了节点数据框中特定的空白标签（第46行），然后像往常一样运行了其余部分。

这是最初的节点文件，以便您可以看到它创建的空白节点，然后我有代码来删除它。请注意，我还添加了一行代码来将列重命名为'名称'：

  1. 1           G. aoyagii
  2. 2         G. axillaris
  3. 3        G. bilineatus
  4. 4           G. brochus
  5. 5     G. erythrospilus
  6. 6        G. fuscoruber
  7. 7           G. histrio
  8. 8     G. oculolineatus
  9. 9  G. quinquestrigatus
  10. 10        G. rivulatus
  11. 11       A. nasuta2014
  12. 12       A. tenuis2014
  13. 13    A. millepora2014
  14. 14   A. torresiana2014
  15. 15         A. spp.2014
  16. 16     A. cerealis2014
  17. 17      A. loripes2014
  18. 18      A. rosaria2014
  19. 19    A. gemmifera2014
  20. 20       A. valida2014
  21. 21       A. tenuis2015
  22. 22       A. nasuta2015
  23. 23    A. millepora2015
  24. 24     A. cerealis2015
  25. 25       A. valida2015
  26. 26   A. torresiana2015
  27. 27         A. spp.2015
  28. 28    A. gemmifera2015
  29. 29      A. loripes2015
  30. 30      A. rosaria2015
  31. 31       A. nasuta2016
  32. 32       A. tenuis2016
  33. 33    A. millepora2016
  34. 34     A. cerealis2016
  35. 35    A. gemmifera2016
  36. 36      A. loripes2016
  37. 37       A. valida2016
  38. 38   A. torresiana2016
  39. 39         A. spp.2016
  40. 40      A. rosaria2016
  41. 41       A. nasuta2018
  42. 42       A. tenuis2018
  43. 43       A. valida2018
  44. 44     A. cerealis2018
  45. 45      A. loripes2018
  46. 46                    
  47. 47      A. rosaria2018
  48. 48    A. gemmifera2018
  49. 49         A. spp.2018
  50. 50       A. selago2018
  51. 51    A. millepora2018
  52. 52       A. nasuta2020
  53. 53     A. cerealis2020
  54. 54         A. spp.2020
  55. 55       A. selago2020
  56. 56      A. loripes2020
  57. 57      A. rosaria2020
  58. 58       A. tenuis2020
  59. 59       A. valida2020
  60. 60    A. millepora2020
  61. 61    A. gemmifera2020
  62. #现在已删除NA节点
  63. #删除NA节点
  64. nodes_test = data.frame(nodes_test[-c(46),])
  65. #重命名列
  66. colnames(nodes_test)[1]='名称'
英文:

I figured it out, so I am posting here in case someone else has the same problem. When generating the node file, the code automatically generated a node for the blanks in certain cells. That node was a blank label in the node dataframe (here in nodes_test dataframe). So I removed the specific blank label (row 46) in the nodes dataframe and ran the rest as usual.

Sankey plot with plotly in R: how do I get the plot to skip over the NAs and not try to plot dead ends of some nodes?

Here is the nodes file initially so you can see the blank node that it created and then I have the code to remove it. Note, I also added a line of code that renamed the column to 'name':

  1. 1           G. aoyagii
  2. 2         G. axillaris
  3. 3        G. bilineatus
  4. 4           G. brochus
  5. 5     G. erythrospilus
  6. 6        G. fuscoruber
  7. 7           G. histrio
  8. 8     G. oculolineatus
  9. 9  G. quinquestrigatus
  10. 10        G. rivulatus
  11. 11       A. nasuta2014
  12. 12       A. tenuis2014
  13. 13    A. millepora2014
  14. 14   A. torresiana2014
  15. 15         A. spp.2014
  16. 16     A. cerealis2014
  17. 17      A. loripes2014
  18. 18      A. rosaria2014
  19. 19    A. gemmifera2014
  20. 20       A. valida2014
  21. 21       A. tenuis2015
  22. 22       A. nasuta2015
  23. 23    A. millepora2015
  24. 24     A. cerealis2015
  25. 25       A. valida2015
  26. 26   A. torresiana2015
  27. 27         A. spp.2015
  28. 28    A. gemmifera2015
  29. 29      A. rosaria2015
  30. 30      A. loripes2015
  31. 31       A. nasuta2016
  32. 32       A. tenuis2016
  33. 33    A. millepora2016
  34. 34     A. cerealis2016
  35. 35    A. gemmifera2016
  36. 36      A. loripes2016
  37. 37       A. valida2016
  38. 38   A. torresiana2016
  39. 39         A. spp.2016
  40. 40      A. rosaria2016
  41. 41       A. nasuta2018
  42. 42       A. tenuis2018
  43. 43       A. valida2018
  44. 44     A. cerealis2018
  45. 45      A. loripes2018
  46. 46                    
  47. 47      A. rosaria2018
  48. 48    A. gemmifera2018
  49. 49         A. spp.2018
  50. 50       A. selago2018
  51. 51    A. millepora2018
  52. 52       A. nasuta2020
  53. 53     A. cerealis2020
  54. 54         A. spp.2020
  55. 55       A. selago2020
  56. 56      A. loripes2020
  57. 57      A. rosaria2020
  58. 58       A. tenuis2020
  59. 59       A. valida2020
  60. 60    A. millepora2020
  61. 61    A. gemmifera2020
  62. #NOW WITH NA NODE REMOVED
  63. #remove node that is NA
  64. nodes_test = data.frame(nodes_test[-c(46),])
  65. #rename column
  66. colnames(nodes_test)[1]=&#39;name&#39;

huangapple
  • 本文由 发表于 2023年5月11日 06:48:53
  • 转载请务必保留本文链接：https://go.coder-hub.com/76223055.html
  • na
  • nodes
  • plotly
  • r
  • sankey-diagram
匿名

发表评论

匿名网友

:?: :razz: :sad: :evil: :!: :smile: :oops: :grin: :eek: :shock: :???: :cool: :lol: :mad: :twisted: :roll: :wink: :idea: :arrow: :neutral: :cry: :mrgreen:

确定