2

我目前正在尝试使用 vegan 包在我的 PCO 图上绘制图例，但图例和图上的 pch 不一样。有谁知道如何解决这个问题？我已经相应地附加了代码和复制数据。非常感谢

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)

以下是复制数据

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)

这是第二个 data.frame

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")
4

1 回答 1

2

在您的legend代码中，levels(MyMeta$Group)表示[1] "Austria" "France" "Germany" "Italy" "Malta" "Spain" "UK". 而是MyMeta$Group0意味着[1] 4 4 6 6 2 2 6 6 6 6 1 2 2 3 ...。pch并且col不被分配到legend. 我介绍了一些解决它的方法。

## 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))

在此处输入图像描述

[@Gavin Simpson 给出的更聪明的方法]

有关更多信息，请参阅评论。

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 回答