Vertex 中的 R iGraph 热图

Question

我对 R 很陌生，并且遇到了一个问题。是否可以在 iGraph 中的顶点上打印热图？我知道我可以做一个彩色的正方形或圆形。但是小型热图可能吗？这是绘制我当前图表的代码:

    # create graph
graph <- graph.data.frame(network[,1:2])
vertex_names <- get.vertex.attribute(graph,"name")


# define node attributes
V(graph)$label.font <- 1
V(graph)$label.font[which(element_types[vertex_names,"type"]=="PRIMARIES")] <- 2
V(graph)$label.font[which(element_types[vertex_names,"type"]=="REACTION")] <- 2

V(graph)$label <- element_types[vertex_names,"label"]
V(graph)$color <- element_types[vertex_names,"color"]
V(graph)$size <- as.integer(element_types[vertex_names,"size"]*20)
V(graph)$label.cex <- element_types[vertex_names,"weight"]

V(graph)$frame.color <- "gray"
V(graph)$frame.color[which(element_types[vertex_names,"type"]=="PRIMARIES")] <- "white"
V(graph)$frame.color[which(element_types[vertex_names,"type"]=="PATHWAY")] <- "white"
V(graph)$frame.color[which(element_types[vertex_names,"type"]=="PRODUCTS")] <- "white"
V(graph)$frame.width <- 10

V(graph)$shape <- "square"
V(graph)$shape[which(element_types[vertex_names,"type"]=="REACTION")] <- "circle"

V(graph)$label.color <- "black"
V(graph)$label.color[which(element_types[vertex_names,"type"]=="PRIMARIES")] <- "darkred"
V(graph)$label.color[which(element_types[vertex_names,"type"]=="PATHWAY")] <- "darkgreen"
V(graph)$label.color[which(element_types[vertex_names,"type"]=="REACTION")] <- "darkorange3"

E(graph)$color <- "red"
E(graph)$color[which(network[,3]=="out")] <- "blue"
E(graph)$color[which(network[,3]=="external")] <- "darkgreen"
E(graph)$arrow.size <- 0.5

layout <- layout.auto(graph)
plot.igraph(graph,layout=layout,main=pathways[pathway_id,"COMMON-NAME"])

此外，我的列表中有可以绘制成热图的矩阵。这些矩阵如下所示:

[[1]]
     TotalSNP HighSNP ModerateSNP PromotorSNP
[1,]        1       0           0           1
[2,]        3       0           2           1
[3,]        5       0           2           3
[4,]        1       0           0           1
[5,]        7       0           4           3
[6,]        3       0           3           0
[7,]        4       0           1           3
[8,]        3       0           2           1

[[2]]
     TotalSNP HighSNP ModerateSNP PromotorSNP
[1,]        3       0           1           2
[2,]        0       0           0           0

[[3]]
     TotalSNP HighSNP ModerateSNP PromotorSNP
[1,]        0       0           0           0
[2,]        0       0           0           0

有谁知道是否可以将这些矩阵绘制为顶点上的热图？

示例数据:

    FinalList <- list(structure(c(1, 3, 5, 1, 7, 3, 4, 3, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 2, 2, 0, 4, 3, 1, 2, 1, 1, 3, 1, 3, 0, 3, 1), .Dim = c(8L, 
4L), .Dimnames = list(NULL, c("TotalSNP", "HighSNP", "ModerateSNP", 
"PromotorSNP"))), structure(c(3, 0, 0, 0, 1, 0, 2, 0), .Dim = c(2L, 
4L), .Dimnames = list(NULL, c("TotalSNP", "HighSNP", "ModerateSNP", 
"PromotorSNP"))), structure(c(0, 0, 0, 0, 0, 0, 0, 0), .Dim = c(2L, 
4L), .Dimnames = list(NULL, c("TotalSNP", "HighSNP", "ModerateSNP", 
"PromotorSNP"))))

矩阵的大小可以变化，始终为 4 列，但行数可以从 0 行到 10 行变化。

Answer 1

因此，正如我在上面的评论中所说，使用新的顶点形状 API 相对容易，尽管您需要了解一些技巧。 igraph 中有一些示例形状，我想这些会有帮助。

所以你需要定义一个函数来绘制你的顶点。它必须具有三个参数:矩阵中的坐标、要绘制的顶点(NULL 表示全部)以及可用于查询 igraph 图形参数的函数对象。如果您有兴趣，请查看代码中的详细信息。如果您想更改热图的外观，只需将 image() 更改为您喜欢的任何内容即可。

myheat <- function(coords, v=NULL, params) {
  colbar <- heat.colors(50)
  colbreaks <- seq(0, 1, length=length(colbar)+1)
  vertex.size <- 1/200 * params("vertex", "size")
  if (length(vertex.size) != 1 && !is.null(v)) {
    vertex.size <- vertex.size[v]
  }
  heat <- params("vertex", "heat")
  if (is.list(heat) && !is.null(v)) {
    heat <- heat[v]
  } else if (!is.null(v)) {
    heat <- list(heat)
  }
  mapply(coords[,1], coords[,2], vertex.size*2, heat,
         FUN=function(x, y, size, int) {
           stopifnot(is.matrix(int))
           nc <- ncol(int); nr <- nrow(int)
           xc <- seq(x, x+size/nc*(nc-1), length=nc)-size/nc*(nc-1)/2
           yc <- seq(y, y+size/nr*(nr-1), length=nr)-size/nr*(nr-1)/2
           image(xc, yc, int, add=TRUE, col=colbar, breaks=colbreaks)
         })
}

# OK, we add the new shape now, it will be called "heat", 
# and will have an extra vertex parameter, also called "heat". 
# This parameter gives the heatmap intensities. The shape will 
# clip as a square, ie. the edges will be cut at the boundary 
# of the heatmap.

add.vertex.shape("heat", clip=vertex.shapes("square")$clip, plot=myheat,
                 parameters=list(vertex.heat=matrix(0,3,3)))

# Some example data and random heatmaps

g <- graph.formula(A:B -+ C:D +- E)
randheat <- function() matrix(runif(9), 3)
heats <- lapply(1:vcount(g), function(x) randheat())

# Plot them

plot(g, vertex.shape="heat", vertex.heat=heats, vertex.size=50)

# You can mix various vertex shapes

par(mar=c(0,0,0,0)+.1)
plot(g, vertex.shape=c("heat", "heat", "sphere", "heat", "heat"),
     vertex.heat=heats, vertex.size=50)