这是我正在尝试绘制的 tidygraph 对象
hub_plot1
# A tbl_graph: 50 nodes and 540 edges
#
# An undirected simple graph with 2 components
#
# Node Data: 50 × 4 (active)
name mod kme color
<chr> <chr> <dbl> <chr>
1 CTSZ turquoise 0.908 black
2 ATP6V0D1 turquoise 0.887 black
3 S100A6 turquoise 0.886 black
4 NADK turquoise 0.869 black
5 PILRA turquoise 0.869 black
6 SIRPA turquoise 0.868 black
# … with 44 more rows
#
# Edge Data: 540 × 3
from to weight
<int> <int> <dbl>
1 1 2 0.587
2 1 3 0.493
3 1 4 0.641
# … with 537 more rows
就像在我的 hubplot 对象中一样，我有两个模块。我的目标是将来自特定模块的所有节点着色为相同的颜色，例如这里我的第一个模块是turquoise我想将它们标记为相同的颜色，这是我用来生成最终图的代码，其中生成了我想要的图形网络，但节点颜色和图例颜色我无法匹配。
sigmods <- c("turquoise","blue") ## modules to plot
lapply(sigmods, function(col) {
maxsize <- 25
hubs <- data.frame(genes=hubgenes[[col]]$gene[1:maxsize], kme = hubgenes[[col]]$kme[1:maxsize], mod = rep(col,25))
}) %>% bind_rows() -> hub_plot1
adj[hub_plot1$genes, hub_plot1$genes] %>%
graph.adjacency(mode = "undirected", weighted = T, diag = FALSE) %>%
as_tbl_graph(g1) %>% upgrade_graph() %>% activate(nodes) %>% dplyr::mutate(mod=hub_plot1$mod) %>%
dplyr::mutate(kme=hub_plot1$kme) %>% activate(edges) %>% dplyr::filter(weight>.15) %>% activate(nodes) %>%
filter(!node_is_isolated()) %>%
dplyr::mutate(color = ifelse(name %in% c("YPEL1","MEGF6","SYNE1","SLC25A23","BCAR1"), yes="red", no="black")) -> hub_plot1
## code to plot
geneplot <- ggraph(hub_plot1, layout = 'fr') +
geom_edge_link(color="darkgrey", aes(alpha = weight), show.legend = F) +
scale_edge_width(range = c(0.2, 1)) + geom_node_text(aes(label = name, color=color), size=3, repel=T) +
geom_node_point(aes(fill = mod, size=kme), shape=21, alpha=0.5) +
scale_size(range = c(1,5), name = "kME") +
ggsci::scale_fill_npg(name="Module") +
# guides(fill = guide_legend(override.aes = list(size=5)),
# size = guide_legend(override.aes = list(size=c(1,2,3,4)))) +
theme_graph(base_family="sans",base_size = 40)+ theme(legend.title.align=0.5,
legend.box = "horizontal",
legend.position = c(0.9, 0.9),
legend.margin = margin(-0.5,0,0,0, unit="cm"),
legend.title = element_text(size=10),
legend.text = element_text(size=8)) +
scale_color_manual(values=c("gray0","red")) + guides(color=FALSE) +
coord_cartesian(clip="off")
我在这里生成的图我们可以看到蓝色模块的颜色不是蓝色而是红色！或橙色不确定。
QUESTION如何匹配节点和图例颜色？任何建议或帮助将非常感激
UPDATE data
dput(hub_plot1)
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