R iGraph顶点热图 [英] R iGraph Heatmap in Vertex

问题描述

我是R的新手，他一直在问一个问题. 是否可以在iGraph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，可能会有小的热图吗? 这是绘制我当前图形的代码:

I'm quite new to R and stuck on a question. Would it be possible to print a heatmap on a vertex in iGraph? I know I can do a colored square or circle. But would a small heatmap be possible? This is the code that draws my current graph:

    # 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，我在列表中有矩阵，可以将其绘制到热图中. 这些矩阵如下所示:

Furthermore, I have matrices in a list that can be drawn into a heatmap. These matrices look like this:

[[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

有人知道是否有可能在顶点上绘制这些矩阵作为热图?

Does anyone know if it's possible to draw these matrices as heatmaps on the vertex?

样本数据:

    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.

The size of the matrices can vary, It's always 4 columns but the number of rows can vary from 0 rows till 10.

推荐答案

因此，正如我在上面的评论中所述，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，我想这些可以帮忙.

So, as I said in the comment above, this is relatively easy with the new vertex shape API, although there are some tricks that you need to know. There are some example shapes in igraph, those help I guess.

因此，您需要定义一个将绘制顶点的函数.它必须具有三个参数，即矩阵中的坐标，要绘制的顶点(NULL表示所有顶点)和一个可用于查询igraph图形参数的函数对象.如果您有兴趣，请参阅代码中的详细信息.如果要更改热图的外观，只需将image()更改为所需的值即可.

So you need to define a function that will plot your vertices. It must have three parameters, the coordinates in a matrix, the vertices to plot (NULL means all of them) and a function object that you can use to query igraph graphics parameters. Please see the details in the code if you are interested. If you want to change the look of the heatmaps, just change image() to whatever you like.

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)

这篇关于R iGraph顶点热图的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！