Must request at least one colour from a hue palette.

[shaodongyan]

I used the data from https://raw.githubusercontent.com/taowenmicro/R-_function/main/. R script is: metadata = read.delim("./metadata.tsv",row.names = 1) otutab = read.delim("./otutab.txt", row.names=1) taxonomy = read.table("./taxonomy.txt", row.names=1)

tree = read_tree("./otus.tree")

rep = readDNAStringSet("./otus.fa")

ps = phyloseq(sample_data(metadata), otu_table(as.matrix(otutab), taxa_are_rows=TRUE), tax_table(as.matrix(taxonomy))#,

phy_tree(tree),

          # refseq(rep)

)

-提取丰度最高的指定数量的otu进行构建网络

----------计算相关#----

result = corMicro (ps = ps, N = 150, method.scale = "TMM", r.threshold=0.8, p.threshold=0.05, method = "spearman"

)

--提取相关矩阵

cor = result[[1]] head(cor)

-网络中包含的OTU的phyloseq文件提取

ps_net = result[[3]]

-导出otu表格

otu_table = ps_net %>% vegan_otu() %>% t() %>% as.data.frame()

netClu = data.frame(ID = row.names(otu_table),group =rep(1:5,length(row.names(otu_table)))[1:length(row.names(otu_table))] ) netClu$group = as.factor(netClu$group) head(netClu)

--------计算布局#---------

result2 = PolygonClusterG (cor = cor,nodeGroup =netClu ) node = result2[[1]] head(node) edge = edgeBuild(cor = cor,node = node) head(edge) p <- ggplot() + geom_segment(aes(x = X1, y = Y1, xend = X2, yend = Y2,color = as.factor(cor)), data = edge, size = 0.5) + geom_point(aes(X1, X2,fill = Phylum,size = mean),pch = 21, data = nodes) + scale_colour_brewer(palette = "Set1") + scale_x_continuous(breaks = NULL) + scale_y_continuous(breaks = NULL) + theme(panel.background = element_blank()) + theme(axis.title.x = element_blank(), axis.title.y = element_blank()) + theme(legend.background = element_rect(colour = NA)) + theme(panel.background = element_rect(fill = "white", colour = NA)) + theme(panel.grid.minor = element_blank(), panel.grid.major = element_blank()) p

But can't plot . Error is Must request at least one colour from a hue palette.