This is my tidygraph object which I'm trying to plot
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
Here as in my hubplot object i have two modules. My objective is to color all the nodes coming from a particular modules as the same color for example here my first module is turquoise
I would like to label them the same color, here is the code which I'm using to generate the final plot where my desired graph network is generated but the node color and the legend color I'm not able to match.
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")
My figure generated here we can see the blue module is colored not blue rather red! or orange not sure.
QUESTION How do I match node and the legend color? any suggestion or help would be really appreciated
UPDATE data
dput(hub_plot1)
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))), <environment>), class = c("tbl_graph", "igraph"), active = "nodes")
Alternatively, if you are looking to use the value in mod as the fill color, you can do so by setting the fill value to the column outside of the aes(). In this case you don't get a legend.
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(size=kme), fill = V(hub_plot1)$mod, shape=21, alpha=0.5) +
scale_size(range = c(1,5), name = "kME") +
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="none") +
coord_cartesian(clip="off")