r - 如何在 map 上以最少的重叠绘制网络

Question

我有一些作者所在的城市或国家。我想知道是否可以在 map 上绘制合著者的网络(图 1)，其中包含国家的坐标。请考虑来自同一国家/地区的多个作者。 [编辑:可以像示例中那样生成多个网络，并且不应显示可避免的重叠]。这是为数十位作者准备的。缩放选项是可取的。为了 future 更好的答案，赏金 promise +100。

refs5 <- read.table(text="
                    row          bibtype year volume   number    pages      title          journal                          author
                    Bennett_1995 article 1995     76    <NA> 113--176 angiosperms.  \"Annals of Botany\"           \"Bennett Md, Leitch Ij\"
                    Bennett_1997 article 1997     80       2 169--196 estimates.  \"Annals of Botany\"           \"Bennett MD, Leitch IJ\"
                    Bennett_1998 article 1998     82 SUPPL.A 121--134 weeds.  \"Annals of Botany\" \"Bennett MD, Leitch IJ, Hanson L\"
                    Bennett_2000 article 2000     82 SUPPL.A 121--134 weeds.  \"Annals of Botany\" \"Bennett MD, Someone IJ\"
                    Leitch_2001 article 2001     83 SUPPL.A 121--134 weeds.  \"Annals of Botany\" \"Leitch IJ, Someone IJ\"
                    New_2002 article 2002     84 SUPPL.A 121--134 weeds.  \"Annals of Botany\" \"New IJ, Else IJ\"" , header=TRUE,stringsAsFactors=FALSE)

rownames(refs5) <- refs5[,1]
refs5<-refs5[,2:9]
citations <- as.BibEntry(refs5)

authorsl <- lapply(citations, function(x) as.character(toupper(x$author)))
unique.authorsl<-unique(unlist(authorsl))
coauth.table <- matrix(nrow=length(unique.authorsl),
                       ncol = length(unique.authorsl),
                       dimnames = list(unique.authorsl, unique.authorsl), 0)
for(i in 1:length(citations)){
  paper.auth <- unlist(authorsl[[i]])
  coauth.table[paper.auth,paper.auth] <- coauth.table[paper.auth,paper.auth] + 1
}
coauth.table <- coauth.table[rowSums(coauth.table)>0, colSums(coauth.table)>0]
diag(coauth.table) <- 0
coauthors<-coauth.table

bip = network(coauthors,
              matrix.type = "adjacency",
              ignore.eval = FALSE,
              names.eval = "weights")

authorcountry <- read.table(text="
 author country
1    \"LEITCH IJ\"     Argentina
2    \"HANSON L\"          USA
3    \"BENNETT MD\"       Brazil
4    \"SOMEONE IJ\"       Brazil
5    \"NEW IJ\"           Brazil
6    \"ELSE IJ\"          Brazil",header=TRUE,fill=TRUE,stringsAsFactors=FALSE)


matched<-   authorcountry$country[match(unique.authorsl, authorcountry$author)]

bip %v% "Country" = matched
colorsmanual<-c("red","darkgray","gainsboro")
names(colorsmanual) <- unique(matched)

gdata<- ggnet2(bip, color = "Country", palette = colorsmanual, legend.position = "right",label = TRUE,  
               alpha = 0.9, label.size = 3, edge.size="weights", 
               size="degree", size.legend="Degree Centrality") + theme(legend.box = "horizontal")
gdata

换句话说，就是在 map 上添加作者姓名、线条和气泡。请注意，多名作者可能来自同一城市或国家，并且不应重叠。 图1 组网

编辑:当前的 JanLauGe 答案与两个不相关的网络重叠。作者“ELSE”和“NEW”需要与其他人分开，如图 1 所示。

Answer 1

您是否正在寻找完全使用您所使用的软件包的解决方案，或者您是否愿意使用其他软件包套件？下面是我的方法，其中我从 network 对象中提取图形属性，并使用 ggplot2 和 map 包将它们绘制在 map 上。

<小时/>

首先，我重新创建您提供的示例数据。

library(tidyverse)
library(sna)
library(maps)
library(ggrepel)
set.seed(1)

coauthors <- matrix(
  c(0,3,1,1,3,0,1,0,1,1,0,0,1,0,0,0),
  nrow = 4, ncol = 4, 
  dimnames = list(c('BENNETT MD', 'LEITCH IJ', 'HANSON L', 'SOMEONE ELSE'),
                  c('BENNETT MD', 'LEITCH IJ', 'HANSON L', 'SOMEONE ELSE')))

coords <- data_frame(
  country = c('Argentina', 'Brazil', 'USA'),
  coord_lon = c(-63.61667, -51.92528, -95.71289),
  coord_lat = c(-38.41610, -14.23500, 37.09024))

authorcountry <- data_frame(
  author = c('LEITCH IJ', 'HANSON L', 'BENNETT MD', 'SOMEONE ELSE'),
  country = c('Argentina', 'USA', 'Brazil', 'Brazil'))

现在我使用 snp 函数 network 生成图形对象

# Generate network
bip <- network(coauthors,
               matrix.type = "adjacency",
               ignore.eval = FALSE,
               names.eval = "weights")

# Graph with ggnet2 for centrality
gdata <- ggnet2(bip, color = "Country", legend.position = "right",label = TRUE,  
               alpha = 0.9, label.size = 3, edge.size="weights", 
               size="degree", size.legend="Degree Centrality") + theme(legend.box = "horizontal")

从网络对象中我们可以提取每条边的值，从ggnet2对象中我们可以得到节点的中心度，如下所示:

# Combine data
authors <- 
  # Get author numbers
  data_frame(
    id = seq(1, nrow(coauthors)),
    author = sapply(bip$val, function(x) x$vertex.names)) %>%
  left_join(
    authorcountry,
    by = 'author') %>%
  left_join(
    coords,
    by = 'country') %>%
  # Jittering points to avoid overlap between two authors
  mutate(
    coord_lon = jitter(coord_lon, factor = 1),
    coord_lat = jitter(coord_lat, factor = 1))

# Get edges from network
networkdata <- sapply(bip$mel, function(x) 
  c('id_inl' = x$inl, 'id_outl' = x$outl, 'weight' = x$atl$weights)) %>%
  t %>% as_data_frame

dt <- networkdata %>%
  left_join(authors, by = c('id_inl' = 'id')) %>%
  left_join(authors, by = c('id_outl' = 'id'), suffix = c('.from', '.to')) %>%
  left_join(gdata$data %>% select(label, size), by = c('author.from' = 'label')) %>%
  mutate(edge_id = seq(1, nrow(.)),
         from_author = author.from,
         from_coord_lon = coord_lon.from,
         from_coord_lat = coord_lat.from,
         from_country = country.from,
         from_size = size,
         to_author = author.to,
         to_coord_lon = coord_lon.to,
         to_coord_lat = coord_lat.to,
         to_country = country.to) %>%
  select(edge_id, starts_with('from'), starts_with('to'), weight)

现在看起来应该像这样:

dt
# A tibble: 8 × 11
  edge_id  from_author from_coord_lon from_coord_lat from_country from_size    to_author to_coord_lon
    <int>        <chr>          <dbl>          <dbl>        <chr>     <dbl>        <chr>        <dbl>
1       1   BENNETT MD      -51.12756     -16.992729       Brazil         6    LEITCH IJ    -65.02949
2       2   BENNETT MD      -51.12756     -16.992729       Brazil         6     HANSON L    -96.37907
3       3   BENNETT MD      -51.12756     -16.992729       Brazil         6 SOMEONE ELSE    -52.54160
4       4    LEITCH IJ      -65.02949     -35.214117    Argentina         4   BENNETT MD    -51.12756
5       5    LEITCH IJ      -65.02949     -35.214117    Argentina         4     HANSON L    -96.37907
6       6     HANSON L      -96.37907      36.252312          USA         4   BENNETT MD    -51.12756
7       7     HANSON L      -96.37907      36.252312          USA         4    LEITCH IJ    -65.02949
8       8 SOMEONE ELSE      -52.54160      -9.551913       Brazil         2   BENNETT MD    -51.12756
# ... with 3 more variables: to_coord_lat <dbl>, to_country <chr>, weight <dbl>

现在继续在 map 上绘制这些数据:

world_map <- map_data('world') 
myMap <- ggplot() +
  # Plot map
  geom_map(data = world_map, map = world_map, aes(map_id = region),
           color = 'gray85',
           fill = 'gray93') +
  xlim(c(-120, -20)) + ylim(c(-50, 50)) + 
  # Plot edges
  geom_segment(data = dt, 
               alpha = 0.5,
               color = "dodgerblue1",
               aes(x = from_coord_lon, y = from_coord_lat,
                   xend = to_coord_lon, yend = to_coord_lat,
                   size = weight)) +
  scale_size(range = c(1,3)) +
  # Plot nodes
  geom_point(data = dt,
             aes(x = from_coord_lon,
                 y = from_coord_lat,
                 size = from_size,
                 colour = from_country)) +
  # Plot names
  geom_text_repel(data = dt %>% 
                    select(from_author, 
                           from_coord_lon, 
                           from_coord_lat) %>% 
                    unique,
                  colour = 'dodgerblue1',
                  aes(x = from_coord_lon, y = from_coord_lat, label = from_author)) + 
  coord_equal() +
  theme_bw()

显然，您可以使用 ggplot2 语法以通常的方式更改颜色和设计。请注意，您还可以使用geom_curve 和arrow 美学来获得类似于上面评论中链接的 super 帖子中的绘图。