ggplot_stat_density2d用于生态分布

Question

我试图描绘我正在阿拉伯/波斯湾研究的某些生物的生态分布.以下是我尝试过的代码示例:

背景层

library(ggplot2)
library(ggmap)

nc <- get_map("Persian Gulf", zoom = 6, maptype = 'terrain', language = "English")
ncmap <- ggmap(nc,  extent = "device")

其他层

  ncmap+
    stat_density2d(data=sample.data3, aes(x=long, y=lat, fill=..level.., alpha=..level..),geom="polygon")+
    geom_point(data=sample.data3, aes(x=long, y=lat))+
    geom_point(aes(x =50.626444, y = 26.044472), color="red", size = 4)+
    scale_fill_gradient(low = "green", high = "red") + scale_alpha(range = c(0.00, 0.25), guide = FALSE)

但是,我想用它stat_density2d来显示数百种物种的分布(在列中记录,例如SP1 ...... SPn),而不仅仅是显示纬度和经度.

此外,是否可以将我的热图限制在水体中？我将非常感谢我能得到的任何帮助和建议

Answer 1

我对你的问题的处理方法是一种务实的方法：只需将海湾国家层放在热图分布上即可。这会相应地裁剪热图。但请注意，热图仍按未裁剪的方式进行计算。这意味着密度计算不仅限于水体，而是简单地在视觉上进行裁剪。

为了重现性，以下代码假设您已解压.rar@Hammao 提供的文件并在结果文件夹中执行代码Persian Gulf。

# get sample data
sample.data <- read.csv("sample.data3.csv")

现在，我们需要获取海湾国家的国家形状。我rworldmap为此使用该包。

# loading country shapes
library(rworldmap) 

# download map of the world
worldmap <- getMap(resolution = "high") # note that for 'resolution="high"' 
                                        # you also need the "rworldxtra" pkg

# extract Persian Gulf countries...
gulf_simpl <- worldmap[worldmap$SOVEREIGNT == "Oman" | 
                         worldmap$SOVEREIGNT == "Qatar"  |
                         worldmap$SOVEREIGNT == "United Arab Emirates" |
                         worldmap$SOVEREIGNT == "Bahrain" |
                         worldmap$SOVEREIGNT == "Saudi Arabia" |
                         worldmap$SOVEREIGNT == "Kuwait" |
                         worldmap$SOVEREIGNT == "Iraq" |
                         worldmap$SOVEREIGNT == "Iran", ]

# ... and fortify the data for plotting in ggplot2
gulf_simpl_fort <- fortify(gulf_simpl)

# Now read data for the Persian Gulf, which we need to get the distances for
# the extension of the map
PG <- readOGR(dsn = ".", "iho")
PG <- readShapePoly("iho.shp")

PG <- fortify(PG)

现在，只需以正确的顺序绘制图层即可。

# generate plot
ggplot(sample.data) + 

  # first we plot the density...
  stat_density_2d(aes(x = long, y = lat, 
                      fill = ..level..),
                  geom="polygon", 
                  alpha = 0.5) +

  # ... then we plot the points
  geom_point(aes(x = long, y = lat)) +

  # gradient options
  scale_fill_gradient(low = "green", high = "red") + 
  scale_alpha(range = c(0.00, 0.25), guide = FALSE) +

  # and now put the shapes of the gulf states on top
  geom_polygon(data = gulf_simpl_fort, 
               aes(x = long, 
                   y = lat, group = group), 
               color = "black", fill = "white", 
               inherit.aes = F) +

  # now, limit the displayed map only to the gulf 
  coord_equal(xlim = c(min(PG_fort$long), max(PG_fort$long)), 
              ylim = c(min(PG_fort$lat), max(PG_fort$lat))) +
  theme_bw()