r - R 中网络图的自定义线条样式

Question

我希望沿着线的长度制作一个带有箭头(或类似的 V 形)的有向网络图...

igraph 库似乎使用基本的 polygon 函数，它接受 lty 来指定线类型，但这些仅限于各种破折号。

有没有办法制作自定义符号(甚至使用pch中的三角形)在R中形成一条线？

制作图表的最少代码:

require(igraph)
gr = graph_from_literal( A -+ B -+ C )
plot(gr,edge.curved=TRUE)

顺便说一句，如果另一个网络分析库支持这一点，我会很好地使用它。我询问了 ggraph 的开发者，他说无法做到这一点。

Answer 1

Cytoscape 和 RCy3 库用于创建网络图。

安装 cytoscape 版本 3 及更高版本 from here 。然后启动 cytoscape GUI(图形用户界面) session 。

此答案中使用的

版本为cytoscape: 3.4.0和RCy3: 1.5。 2

操作系统:Windows-7

# load libraries
library('RCy3')

# create cytoscape connection
cy <- RCy3::CytoscapeConnection()
RCy3::deleteAllWindows(cy)       # delete all windows in cytoscape
hideAllPanels(cy)                # hide all panels

# create node and edge data and create graphNEL object
node.tbl <- data.frame(Node.Name = c('A', 'B', 'C'))
edge.tbl <- data.frame(Gene.1 = c('A', 'B'),
                       Gene.2 = c('B', 'C'))
g <- cyPlot(node.tbl, edge.tbl)
g
# A graphNEL graph with directed edges
# Number of Nodes = 3 
# Number of Edges = 2 

# create cytoscape window and display the graph
window_title <- 'example'
cw <- RCy3::CytoscapeWindow(window_title, graph=g, overwrite=FALSE)
RCy3::displayGraph(cw)

# set visual style and layout algorithm
vis_style <- 'Curved'               # getVisualStyleNames(cw)[7]
RCy3::setVisualStyle(cw, vis_style)       
RCy3::layoutNetwork(obj = cw, layout.name = "circular")
RCy3::layoutNetwork(obj = cw, layout.name = "kamada-kawai")

# get all edges
getAllEdges(cw)
# [1] "A (unspecified) B" "B (unspecified) C"

# get cytoscape supported line types
supported_styles <- getLineStyles (cw)
supported_styles
# [1] "EQUAL_DASH"       "PARALLEL_LINES"   "MARQUEE_DASH"     "MARQUEE_EQUAL"    "SOLID"            "FORWARD_SLASH"    "DASH_DOT"         "MARQUEE_DASH_DOT"
# [9] "SEPARATE_ARROW"   "VERTICAL_SLASH"   "DOT"              "BACKWARD_SLASH"   "SINEWAVE"         "ZIGZAG"           "LONG_DASH"        "CONTIGUOUS_ARROW"

# set edge line type
setEdgeLineStyleDirect(cw, "A (unspecified) B", supported_styles [16])  # "CONTIGUOUS_ARROW"

setEdgeLineStyleDirect(cw, "A (unspecified) B", supported_styles [9])   # "SEPARATE_ARROW"

# save network as image in the current working directory
fitContent (cw)
setZoom(cw, getZoom(cw) - 1)  # adjust the value from 1 to a desired number to prevent cropping of network diagram
saveImage(obj = cw, 
          file.name = 'example',
          image.type = 'png',
          h = 700)

有关详细信息，请阅读?RCy3::setEdgeLineStyleDirect。

另外，对于 cytoscape 边缘属性，请参阅 here

安装 RCy3:

# Install RCy3 - Interface between R and Cytoscape (through cyRest app)
library('devtools')

remove.packages("BiocInstaller")
source("https://bioconductor.org/biocLite.R")
biocLite("BiocGenerics")
biocLite("bitops")
install_github("tmuetze/Bioconductor_RCy3_the_new_RCytoscape")