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.