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====== 宏基因组物种top10全层级桑基流向图（sankeyD3） ======
展示种水平的物种在全部层级上的丰度信息

===== 输入数据 =====
分组信息：group.list
<code>
B001	G1
B002	G1
B003	G1
B004	G1
B005	G1
B006	G1
</code>
指定物种的全部层级信息：tax.txt
<code>
k__Bacteria;p__Chlamydiae;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydia;s__Chlamydia abortus
k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas;s__Pseudomonas fragi
k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli
</code>
标准交付结果中：Unigenes.absolute.total.tax.xls

===== 输出数据后需要手动整理一下 =====
<code>
#这一部分待完善
source	target	value
Bacteria	Proteobacteria	259448081
Proteobacteria	Gammaproteobacteria	236402001.9
Gammaproteobacteria	Pseudomonadales	152013077
Pseudomonadales	Pseudomonadaceae	74632447.24
Pseudomonadaceae	Pseudomonas	74603074.6
Pseudomonas	Pseudomonas fragi	16409742.58
Bacteria	Chlamydiae	28479113.74
Chlamydiae	Chlamydiia	28478395.54
Chlamydiia	Chlamydiales	28474661.59
Chlamydiales	Chlamydiaceae	28472728.3
Chlamydiaceae	Chlamydia	28472724.78
Chlamydia	Chlamydia abortus	22096800.37

</code>

===== 在本地安装并调用sankeyD3 =====

<code>
#setwd("E:\\personal_demand\\sankeyd3\\sankey20230509-G2")
require(sankeyD3)
require(xlsx)
require(magrittr)
require(webshot)
#shiny::runGitHub("fbreitwieser/sankeyD3", subdir="inst/examples/shiny")
#URL <- paste0("https://cdn.rawgit.com/christophergandrud/networkD3/",
#              "master/JSONdata/energy.json")
#Energy <- jsonlite::fromJSON(URL)

# Plot
links <- read.xlsx("result.xlsx",sheetIndex = 1)

nodes <- data.frame(name=c(as.character(links$source), as.character(links$target)) %>% unique())

links$IDsource <- match(links$s, nodes$name)-1

links$IDtarget <- match(links$t, nodes$name)-1

p <- sankeyNetwork(Links = links, Nodes = nodes, 
                   Source = "IDsource", Target = "IDtarget",
                   Value = "value", NodeID = "name",
                   nodeWidth =15,units = 'TWh',
                   colourScale = JS("d3.scaleOrdinal().range(d3.schemeCategory20)"),
                   numberFormat=".0f",fontSize = 10,
                   nodeCornerRadius=3,nodeShadow = T,
#                   linkColor = "Source",
                   height=600,width=1200)
p
saveNetwork(p,"sankeyG2.html")

#webshot("sankeyG2.html" , "sankey.pdf",vwidth = 100,vheight = 50)
</code>

===== 最终结果展示 =====

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