在ggplot2中指定特定形状

Question

我有一个DCA图，我已经告诉ggplot2根据它们来自的网站给出不同的形状。我想用一个不同的变量填充它，所以我需要15-25的形状。如何告诉ggplot2选择“可填充”的符号？我目前不得不使用colour=regforamcountsall$SWLI，但我知道一旦我可以使用正确的符号，它就会变成fill。

library(vegan)
library(ggplot2)
library(cluster)
library(ggfortify)
library(factoextra)

regforamcountsall<-read.csv("regionalforamscountsall.csv",header=TRUE)


regforamcountsall$Sample = NULL
regforamcountsall$Site=NULL
regforamcountsall$SWLI=NULL



#Run DCA
ord <- decorana(regforamcountsall)

plot(ord)

#use this summary code to get species scores for DCA1 and DCA2

summary(ord)

#put species scores values in from ord plot summary stats 
species.scores<-read.csv("speciesscores.csv")


species.scores$species <- row.names(species.scores)

#Using the scores function from vegan to extract the sample scores and convert to a data.frame
data.scores <- as.data.frame(scores(ord))  

# create a column of groupings/clusters, from the rownames of data.scores
data.scores$endgroup <- as.factor(pam(regforamcountsall, 3)$clustering) 

#getting the convex hull of each unique point set
find_hull <- function(df) df[chull(data.scores$DCA1, data.scores$DCA2), ]
hulls <- NULL
for(i in 1:length(unique(data.scores$endgroup))){
  endgroup_coords <- data.scores[data.scores$endgroup == i,]
  hull_coords <- data.frame(
    endgroup_coords[chull(endgroup_coords[endgroup_coords$endgroup == i,]$DCA1,
                          endgroup_coords[endgroup_coords$endgroup == i,]$DCA2),])
  hulls <- rbind(hulls,hull_coords)
}


data.scores$numbers <- 1:length(data.scores$endgroup)

regforamcountsall<-read.csv("regionalforamscountsall.csv",header=TRUE)

#DCA 
dca <- ggplot() + 
  # add the point markers
geom_point(data=data.scores,aes(x=DCA1,y=DCA2,colour=regforamcountsall$SWLI),size=4,pch=regforamcountsall$Site) +
  geom_point(data=species.scores,aes(x=DCA1,y=DCA2),size=4,pch=18,colour="grey22", alpha=0.8) +
  # add the hulls and labels - numbers position labels
  geom_polygon(data = hulls,aes(x=DCA1,y=DCA2,fill=endgroup), alpha = 0.25) +
  #geom_text(data=data.scores,aes(x=DCA1-0.03,y=DCA2,colour=endgroup, label = numbers))+
  geom_text(data=species.scores,aes(x=DCA1+0.1,y=DCA2+0.1, label = species))+
  theme_classic()+
  
dca

structure(list(species = c("1", "2", "3", "4", "5", "6"), DCA1 = c(-2.1171, 
-1.6729, -2.0028, -0.961, 1.0481, -0.3297), DCA2 = c(0.3289, 
-0.839, 0.343, -0.36, 1.9886, 0.9175)), row.names = c(NA, 6L), class = "data.frame")

structure(list(DCA1 = c(-1.13413767300063, -1.71882459720626, 
-1.52607134864953, -1.32194095756686, -1.69520357242868, -0.141922349857954
), DCA2 = c(0.0633645085805346, 0.377157525612764, 0.120142668154026, 
0.174188452426213, -0.00943018635973858, 0.326711919777559), 
    DCA3 = c(0.00488308715045149, -0.749294000660211, -0.480312621168478, 
    -0.170111605941518, 0.0943798426120048, 0.0441643135499474
    ), DCA4 = c(-0.35705788574092, -0.475715464243968, -0.350994520702336, 
    -0.257048075477532, 0.0210812333627229, 0.0754508519926794
    ), endgroup = structure(c(1L, 1L, 1L, 1L, 1L, 2L), .Label = c("1", 
    "2", "3"), class = "factor"), numbers = 1:6), row.names = c(NA, 
6L), class = "data.frame")

structure(list(Sample = structure(c(2L, 23L, 30L, 24L, 25L, 28L
), .Label = c("LG1", "LG120", "LG130", "LG135", "LG160", "LG170", 
"LG185", "LG2", "LG225", "LG230", "LG240", "LG245", "LG255", 
"LG260", "LG275", "LG280", "LG285", "LG290", "LG295", "LG3", 
"LG305", "LG315", "LG32", "LG36", "LG38", "LG4", "LG48", "LG5", 
"LG60", "LG7", "LSP010", "LSP020", "LSP030", "LSP040", "LSP050", 
"LSP060", "LSP070", "LSP080", "LSP089", "LSP100", "LSP110", "LSP120", 
"LSP130", "LSP140", "LSP150", "LSP160", "LSP165", "ST-2LG0", 
"ST-2LG100", "ST-2LG120", "ST-2LG140", "ST-2LG160", "ST-2LG190", 
"ST-2LG40", "ST-2LG60", "ST-2LG80", "T3LB11.301", "T3LB12.05", 
"T3LB12.844", "T3LB13.87", "T3LB14.51", "T3LB14.63", "T3LB15.321", 
"T3LB15.59", "T3LB15.95", "T3LB16.69", "T3LB18.226", "T3LB19.762", 
"T3LB21.078", "T3LB26.256", "T3LB28.57", "T3LB28.84", "T3LB29.03", 
"T3LB31.056", "T3LB31.365", "T3LB7.008", "T3LB7.18", "T3LB7.303", 
"T3LB7.5", "T3LB7.9", "T3LB8.73", "T3LB9.45", "WAP 0 ST-2", "WAP 10 ST-2", 
"WAP 110 ST1", "WAP 120 ST-1", "WAP 122 ST-1", "WAP 125 ST1", 
"WAP 130 ST1", "WAP 135 ST-1", "WAP 140 ST-1", "WAP 144 ST-1", 
"WAP 150 ST-1 ", "WAP 155 ST-1", "WAP 159 ST1", "WAP 160 ST-1", 
"WAP 170 ST-1", "WAP 175 ST 1", "WAP 180 ST-1", "WAP 190 ST-1", 
"WAP 200 ST-1", "WAP 210 ST-1", "WAP 230 ST-1", "WAP 240 ST-1", 
"WAP 25 ST-2", "WAP 40 ST-2", "WAP 45 ST-2", "WAP 5  ST-2", "WAP 50 ST-2", 
"WAP 55 ST-2", "WAP 60 ST-1", "WAP 60 ST-2"), class = "factor"), 
    T.salsa = c(44.4, 75.4, 68, 51.9, 56, 0), H.wilberti = c(9.4, 
    1.8, 8.2, 10.3, 28.8, 0), Textularia = c(0.4, 0, 0, 0, 0, 
    0), T.irregularis = c(0, 3.6, 2.5, 0, 0.4, 0), P.ipohalina = c(0, 
    0, 0, 0, 0, 0), J.macrescens = c(5.4, 17.4, 7.4, 13.4, 6.6, 
    45.5), T.inflata = c(40.4, 1.8, 7.4, 24.4, 8.2, 53), S.lobata = c(0, 
    0, 0, 0, 0, 0), M.fusca = c(0, 0, 6.6, 0, 0, 1.5), A.agglutinans = c(0, 
    0, 0, 0, 0, 0), A.exiguus = c(0, 0, 0, 0, 0, 0), P.hyperhalina = c(0, 
    0, 0, 0, 0, 0), H.germanica = c(0, 0, 0, 0, 0, 0), Quinqueloculina = c(0, 
    0, 0, 0, 0, 0), Elphidium = c(0, 0, 0, 0, 0, 0), SWLI = c(190.4972376, 
    190.3867403, 190.2762431, 188.3977901, 186.8508287, 185.4143646
    ), Site = c(1, 1, 1, 1, 1, 1)), row.names = c(NA, 6L), class = "data.frame")

Answer 1

在通过scale_shape_discrete传递调色板函数时，似乎存在an old bug。因此，这比通常的情况要复杂一些：

#based on example in help("scale_shape")
dsmall <- diamonds[sample(nrow(diamonds), 100), ]

ggplot(dsmall, aes(carat, price, shape = cut, fill = factor(clarity))) + 
  geom_point(size = 5) +
  discrete_scale("shape", "shape", palette=function(n) {
    stopifnot("more than 5 shapes not supported" = n <= 5)
    20 + seq_len(n)
    }) +
  guides(fill = guide_legend(override.aes = list(shape = 21)))

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