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現在、vegan パッケージを使用して PCO グラフに凡例をプロットしようとしていますが、凡例とプロットの pch が同じではありません。この問題を解決する方法を知っている人はいますか？それに応じて、コードとレプリケーション データを添付しました。どうもありがとう

library(vegan)
pco2 <- capscale(vec2 ~ 1, add = TRUE)
pco2
ordiplot(pco2, display = 'sites', type = 'n', cex=.75, main="Biotechnology Dissimilarity")
points (pco2, col = MyMeta$Group0, pch=MyMeta$Group0)
legend(x="bottomleft", legend=levels(MyMeta$Group), col=MyMeta$Group0, pch=MyMeta$Group0)

以下は複製データです

vec2 <- structure(c(5.6e-05, 0.000264854, 0.031144847, 1.36e-05, 0.0077926, 
9.61e-06, 0.018901651, 0.005618188, 0.025462273, 0.078385688, 
0.004847819, 0.017850528, 0.000467735, 5.4e-05, 0.001046951, 
0.006335814, 0.03979001, 6.73e-05, 0.143216374, 0.000402185, 
5.99e-06, 0.008637892, 0.000906473, 0.030147803, 0.000696942, 
0.06038404, 0.000625457, 0.035261238, 0.042930657, 0.01282187, 
0.030221599, 0.000118513, 0.003552078, 0.002547753, 0.005850736, 
0.0001176, 0.001012019, 0.022458292, 0.023196107, 0.061736236, 
0.010543594, 0.032114583, 1.02e-05, 0.013650841, 0.000419571, 
0.000358173, 0.003873999, 0.000165441, 0.027002225, 0.026133375, 
0.028335404, 0.027503738, 0.000136987, 0.001289475, 0.048530267, 
0.000208896, 0.002173612, 0.023953018, 2.3e-05, 0.019027806, 
0.000495739, 0.011051853, 0.021856285, 0.006643201, 0.011511987, 
1.1e-05, 0.002010242, 0.003117657, 0.117475573, 0.024946637, 
0.058560863, 0.102647711, 0.000379362, 0.000603669, 1.97e-05, 
0.020976103, 0.01459725, 0.000289262, 0.003064517, 0.008196972, 
0.000302017, 0.020562333, 0.093245647, 0.008974985, 0.015369811, 
0.013341021, 0.000146334, 0.045070436, 0.002364084, 0.001069053, 
0.000525468, 0.024699631, 0.000210154, 0.013661305, 0.014193045, 
9.36e-05, 0.008298908, 0.001575832, 0.002778748, 0.026456846, 
0.05169889, 0.023670177, 0.000370742, 0.211737239, 0.011322947, 
0.022878397, 1.95e-06, 0.055530173, 2.34e-05, 8.81e-06, 0.000189184, 
0.000270935, 7.4e-05, 0.000178542, 0.000530574, 0.005837658, 
0.024640248, 0.006536165, 0.011476716, 0.003567421, 0.000424627, 
0.000295164, 6.09e-05, 1.02e-05, 0.043852798, 0.033416026, 0.011645167, 
0.000166027, 6.94e-05, 0.042856405, 0.000429471, 0.00051019, 
0.000530227, 0.006190825, 1.75e-05, 0.023080027, 4.07e-05, 0.001322897, 
0.041780286, 0.000358371, 6.89e-05, 3.47e-05, 0.00132758, 0.001339749, 
0.012596551, 0.003345775, 2.54e-05, 0.000660134, 0.031165069, 
0.000149653, 1.09e-05, 0.009427228, 6.33e-05, 0.030851467, 0.009840297, 
0.008769023, 0.006244515, 6.09e-05, 0.001459698, 0.010502741, 
0.00054124, 0.000238582, 0.000303381, 0.019191567, 5.91e-05), class = "dist", Labels = c("Abruzzo07", 
"Abruzzo14", "Andalucia07", "Andalucia14", "Aquitanie07", "Aquitanie14", 
"Aragon07", "Aragon14", "Asturias07", "Asturias14", "Austria07", 
"Austria14", "Auvergne07", "Auvergne14", "Baden-Wu07", "Baden-Wu14", 
"Baleares07", "Baleares14", "Basilicata07", "Basilicata14", "Basse Normandie07", 
"Basse Normandie14", "Bavaria07", "Bavaria14", "Berlin07", "Berlin14", 
"Bolzano07", "Bolzano14", "Bourgogne07", "Bourgogne14", "Bradenburgh07", 
"Bradenburgh14", "Bremen07", "Bremen14", "Bretagne07", "Bretagne14", 
"Burgenland07", "Burgenland14", "Campania07", "Campania14", "Canarias07", 
"Canarias14", "Cantabria07", "Cantabria14", "Carinthia07", "Carinthia14", 
"CastillaLaMancha07", "CastillaLaMancha14", "CastillayLeon07", 
"CastillayLeon14", "Catalonia07", "Catalonia14", "Centre07", 
"Centre14", "Champagne-Ardenne07", "Champagne-Ardenne14", "Corsica07", 
"Corsica14", "EastWales07", "EastWales14", "Emilia Romagna07", 
"Emilia Romagna14", "England07", "England14", "Franche-Comte07", 
"Franche-Comte14", "Friuli Venezia Giulia07", "Friuli Venezia Giulia14", 
"Hamburg07", "Hamburg14", "Haute Normandie07", "Haute Normandie14", 
"Hessen07", "Hessen14", "Italy07", "Italy14", "La Rioja07", "Lazio07", 
"Lazio14", "Liguria07", "Liguria14", "Limousine07", "Limousine14", 
"Loire07", "Loire14", "Lombardy07", "Lombardy14", "Lorraine07", 
"Lorraine14", "Lower Austria07", "Lower Austria14", "Lower Saxony07", 
"Lower Saxony14", "Madrid07", "Madrid14", "Malta07", "Malta14", 
"Marche07", "Marche14", "Mecklenburg-Vorpommern07", "Mecklenburg-Vorpommern14", 
"Midi-Pyrenees07", "Midi-Pyrenees14", "Molise07", "Molise14", 
"Murcia07", "Murcia14", "Calais07", "Calais14", "NorthernIreland07", 
"NorthernIreland14", "Picardie07", "Picardie14", "Piemonte07", 
"Piemonte14", "Poitou-Charentes07", "Poitou-Charentes14", "Puglia07", 
"Puglia14", "Rheinland07", "Rheinland14", "Rhone-Alpes07", "Rhone-Alpes14", 
"Saarland07", "Saarland14", "Salzburg07", "Salzburg14", "Sardinia07", 
"Sardinia14", "Saxony-Anhalt07", "Saxony-Anhalt14", "Saxony07", 
"Saxony14", "Schleswig-Holstein07", "Schleswig-Holstein14", "Scotland07", 
"Scotland14", "Sicily07", "Sicily14", "Steiermark07", "Steiermark14", 
"Thuringia07", "Thuringia14", "Trento07", "Trento14", "Tuscany07", 
"Tuscany14", "Tyrol07", "Tyrol14", "Umbria07", "Umbria14", "Upper Austria07", 
"Upper Austria14", "Valencia07", "Valencia14", "Valle d'Aosta07", 
"Valle d'Aosta14", "Veneto07", "Veneto14", "Vienna07", "Vienna14", 
"Vorarlberg014", "Vorarlberg07", "West Wales07", "West Wales14"
), Size = 165, Diag = FALSE, Upper = FALSE)

これは 2 番目の data.frame です

MyMeta<- structure(list(Group = structure(c(4L, 4L, 6L, 6L, 2L, 2L, 6L, 
6L, 6L, 6L, 1L, 2L, 2L, 3L, 3L, 6L, 6L, 4L, 4L, 2L, 2L, 3L, 3L, 
3L, 3L, 4L, 4L, 2L, 2L, 3L, 3L, 3L, 3L, 2L, 2L, 1L, 1L, 4L, 4L, 
6L, 6L, 6L, 6L, 1L, 1L, 6L, 6L, 6L, 6L, 6L, 6L, 2L, 2L, 2L, 2L, 
2L, 2L, 7L, 7L, 4L, 4L, 7L, 7L, 2L, 2L, 4L, 4L, 3L, 3L, 2L, 2L, 
3L, 3L, 6L, 4L, 4L, 4L, 4L, 2L, 2L, 2L, 2L, 4L, 4L, 2L, 2L, 1L, 
1L, 3L, 3L, 6L, 6L, 5L, 5L, 4L, 4L, 3L, 3L, 2L, 2L, 4L, 4L, 6L, 
6L, 1L, 4L, 4L, 2L, 2L, 7L, 7L, 2L, 2L, 4L, 4L, 2L, 2L, 4L, 4L, 
3L, 3L, 2L, 2L, 3L, 3L, 1L, 1L, 4L, 4L, 3L, 3L, 3L, 3L, 3L, 3L, 
7L, 7L, 4L, 4L, 1L, 1L, 3L, 3L, 4L, 4L, 4L, 4L, 1L, 1L, 4L, 4L, 
1L, 1L, 6L, 6L, 4L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 7L, 7L), .Label = c("Austria", 
"France", "Germany", "Italy", "Malta", "Spain", "UK"), class = "factor"), 
Group0 = c(4, 4, 6, 6, 2, 2, 6, 6, 6, 6, 1, 2, 2, 3, 3, 6, 
6, 4, 4, 2, 2, 3, 3, 3, 3, 4, 4, 2, 2, 3, 3, 3, 3, 2, 2, 
1, 1, 4, 4, 6, 6, 6, 6, 1, 1, 6, 6, 6, 6, 6, 6, 2, 2, 2, 
2, 2, 2, 7, 7, 4, 4, 7, 7, 2, 2, 4, 4, 3, 3, 2, 2, 3, 3, 
6, 4, 4, 4, 4, 2, 2, 2, 2, 4, 4, 2, 2, 1, 1, 3, 3, 6, 6, 
5, 5, 4, 4, 3, 3, 2, 2, 4, 4, 6, 6, 1, 4, 4, 2, 2, 7, 7, 
2, 2, 4, 4, 2, 2, 4, 4, 3, 3, 2, 2, 3, 3, 1, 1, 4, 4, 3, 
3, 3, 3, 3, 3, 7, 7, 4, 4, 1, 1, 3, 3, 4, 4, 4, 4, 1, 1, 
4, 4, 1, 1, 6, 6, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7)), .Names = c("Group", 
"Group0"), row.names = c("Abruzzo07", "Abruzzo14", "Andalucia07", 
"Andalucia14", "Aquitanie07", "Aquitanie14", "Aragon07", "Aragon14", 
"Asturias07", "Asturias14", "Austria07", "Austria14", "Auvergne07", 
"Auvergne14", "Baden-Wu07", "Baden-Wu14", "Baleares07", "Baleares14", 
"Basilicata07", "Basilicata14", "Basse Normandie07", "Basse Normandie14", 
"Bavaria07", "Bavaria14", "Berlin07", "Berlin14", "Bolzano07", 
"Bolzano14", "Bourgogne07", "Bourgogne14", "Bradenburgh07", "Bradenburgh14", 
"Bremen07", "Bremen14", "Bretagne07", "Bretagne14", "Burgenland07", 
"Burgenland14", "Campania07", "Campania14", "Canarias07", "Canarias14", 
"Cantabria07", "Cantabria14", "Carinthia07", "Carinthia14", "CastillaLaMancha07", 
"CastillaLaMancha14", "CastillayLeon07", "CastillayLeon14", "Catalonia07", 
"Catalonia14", "Centre07", "Centre14", "Champagne-Ardenne07", 
"Champagne-Ardenne14", "Corsica07", "Corsica14", "EastWales07", 
"EastWales14", "Emilia Romagna07", "Emilia Romagna14", "England07", 
"England14", "Franche-Comte07", "Franche-Comte14", "Friuli Venezia Giulia07", 
"Friuli Venezia Giulia14", "Hamburg07", "Hamburg14", "Haute Normandie07", 
"Haute Normandie14", "Hessen07", "Hessen14", "Italy07", "Italy14","La Rioja07", "Lazio07", "Lazio14", "Liguria07", "Liguria14", 
"Limousine07", "Limousine14", "Loire07", "Loire14", "Lombardy07", 
"Lombardy14", "Lorraine07", "Lorraine14", "Lower Austria07", 
"Lower Austria14", "Lower Saxony07", "Lower Saxony14", "Madrid07", 
"Madrid14", "Malta07", "Malta14", "Marche07", "Marche14", "Mecklenburg-Vorpommern07", 
"Mecklenburg-Vorpommern14", "Midi-Pyrenees07", "Midi-Pyrenees14", 
"Molise07", "Molise14", "Murcia07", "Murcia14", "Calais07", "Calais14", 
"NorthernIreland07", "NorthernIreland14", "Picardie07", "Picardie14", 
"Piemonte07", "Piemonte14", "Poitou-Charentes07", "Poitou-Charentes14", 
"Puglia07", "Puglia14", "Rheinland07", "Rheinland14", "Rhone-Alpes07", 
"Rhone-Alpes14", "Saarland07", "Saarland14", "Salzburg07", "Salzburg14", 
"Sardinia07", "Sardinia14", "Saxony-Anhalt07", "Saxony-Anhalt14", 
"Saxony07", "Saxony14", "Schleswig-Holstein07", "Schleswig-Holstein14", 
"Scotland07", "Scotland14", "Sicily07", "Sicily14", "Steiermark07", 
"Steiermark14", "Thuringia07", "Thuringia14", "Trento07", "Trento14", 
"Tuscany07", "Tuscany14", "Tyrol07", "Tyrol14", "Umbria07", "Umbria14", 
"Upper Austria07", "Upper Austria14", "Valencia07", "Valencia14", 
"Valle d'Aosta07", "Valle d'Aosta14", "Veneto07", "Veneto14", 
"Vienna07", "Vienna14", "Vorarlberg014", "Vorarlberg07", "West Wales07", 
"West Wales14"), class = "data.frame")
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1 に答える 1

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あなたのlegendコードでは、levels(MyMeta$Group)を意味し[1] "Austria" "France" "Germany" "Italy" "Malta" "Spain" "UK"ます。しかし、MyMeta$Group0意味し[1] 4 4 6 6 2 2 6 6 6 6 1 2 2 3 ...ます。pchにcol割り当てられていませんlegend。解決方法をいくつか紹介しました。

## the most easy method (if your Group0 isn't alphabetical order, this method can't be used.)
legend(x="bottomleft", legend=levels(MyMeta$Group), col=1:7, pch=1:7)
                                 #  you can use seq.int(levels(MyMeta$Group)) instead of 1:7

## a versatile method (this method doesn't need the condition of Group0)
legend(x="top", legend=unique(MyMeta$Group), col=unique(MyMeta$Group0), pch=unique(MyMeta$Group0))

  # if you want alphabetical order,
  library(dplyr)
  MyMeta %>% distinct(Group, Group0) %>% arrange(Group) %>% 
    with(legend(x="bottomright", legend=Group, col=Group0, pch=Group0))

ここに画像の説明を入力

[ @Gavin Simpson が提供したよりスマートな方法]

詳細については、コメントを参照してください。

library(vegan)
pco2 <- capscale(vec2 ~ 1, add = TRUE)

pchv <- 1:7
colv <- 1:7

ordiplot(pco2, display = 'sites', type = 'n', cex=.75, main="Biotechnology Dissimilarity")
with(MyMeta, points(pco2, col=colv[Group], pch=pchv[Group]))
with(MyMeta, legend(x="bottomleft", legend=levels(Group), col=colv, pch=pchv))
于 2016-08-04T02:24:20.923 に答える