热图报错！

[CampingOnSeabed]

您好这是我的代码。
monocle3_genes <- rownames(cds_gene[,c(5,2,3,4,1,6)] %>% filter(q_value < 1e-3 & morans_I >0.19) )
mat <- pre_pseudotime_matrix(cds_obj = cds,
gene_list = monocle3_genes)
head(mat[1:5,1:5])
#getClusters(exp = mat)

ck <- clusterData(exp = mat,
cluster.method = "kmeans",
cluster.num = 3)

add line annotation

markergenes <- c("SOX2","NES","ASCL1","VIM","PAX3","PAX6","PAX7",
"GSX1","GSX2","PAX2","PAX8","LBX1","LHX1","LHX5",
"TLX3","POU4F1","DRGX")
pdf('monocle3.pdf',height = 6,width = 8,onefile = F)
p <- visCluster(object = ck,
cluster.order = c(1,3,2),
plot.type = "both",
add.sampleanno = F,
markGenes = markergenes,
show_row_dend = F)
p
p <-visCluster(object = ck,
plot.type = "both",
add.sampleanno = F,
markGenes = markergenes)
p
#改变row顺序
p1 <- p
p1@ht_list[["Z-score"]]@row_order_list[["C1"]] <- rev(c(1:392))
p1@ht_list[["Z-score"]]@row_order_list[["C3"]] <- rev(c(657:776))
p1@ht_list[["Z-score"]]@row_order_list[["C2"]] <- rev(c(393:656))
pdf('monocle3-1.pdf',height = 6,width = 8,onefile = F)
p1
dev.off()

这步运行完正常产生一个热图
ck <- clusterData(exp = mat,
cluster.method = "kmeans",
cluster.num = 3)
再往下运行就会说
This palatte have 20 colors!
然后热图没有任何变化，请大佬教一下

[junjunlab]

不太明白你要表达什么

[CampingOnSeabed]

博主您好，就是我运行下面这段代码后，出现这个热图
ck <- clusterData(exp = mat,
cluster.method = "kmeans",
cluster.num = 3)

然后接着运行
markergenes <- c("SOX2","NES","ASCL1","VIM","PAX3","PAX6","PAX7",
"GSX1","GSX2","PAX2","PAX8","LBX1","LHX1","LHX5",
"TLX3","POU4F1","DRGX")
p <- visCluster(object = ck,
cluster.order = c(1,3,2),
plot.type = "both",
add.sampleanno = F,
markGenes = markergenes,
show_row_dend = F)
会报出This palatte have 20 colors!
然后会产生

但是理想情况应该是这样的

麻烦您有空的时候解答一下吧，非常感谢！

[junjunlab]

把你的mat发我看看

[CampingOnSeabed]

把你的mat发我看看
你好，非常感谢。但是我的mat.csv有156MB，github发不上来。。。。
请问方便发到您的邮箱嘛

[junjunlab]

pdf函数保存再打开就没问题了。