This palatte have 20 colors! No more than 4 columns! 错误: names of text should have overlap to levels in align_to.

[Jingjing0124]

老师您好 ClusterGVi 最后添加各cluster 富集注释信息时出现 This palatte have 20 colors! No more than 4 columns! 错误: names of text should have overlap to levels in align_to.
请问如何解决

[junjunlab]

请提供你的代码

[Taoli0113]

请提供你的代码

老师您好，我遇到了相同的问题@junjun，我的WGCNA结果总共有26个module，60个样本，包含19200个基因，使用clusterGVis的heatmap可以绘制，但enrichGO以后添加富集功能信息报错，我的代码如下：
library(ClusterGVis)
library(ComplexHeatmap)
library(org.Hs.eg.db)
library(cols4all)

write.csv(datExpr0,"datExpr0.csv")
str(bwnet)

exp <- datExpr0
expt <- t(datExpr0)

get data

cw <- clusterData(exp = exp,
cluster.method = "wgcna",
object = bwnet_filtered)
str(cw)

add gene name

markGenes = rownames(expt)[sample(1:nrow(expt),30,replace = F)]

pdf('./ClusterGVis/GvisCluster_cw_16Area_line.pdf', height = 6, width = 16, onefile = F)
visCluster(
object = cw,
plot.type = "line", #折线图
add.mline = TRUE #是否显示中位折线
)
dev.off()

heatmap

pdf('./ClusterGVis/netht.pdf',height = 10,width = 6,onefile = F)
visCluster(object = cw,
plot.type = "heatmap",
markGenes = markGenes)
dev.off()

GO

enrich <- enrichCluster(object = cw,
OrgDb = org.Hs.eg.db,
type = "BP", #"BP","MF","CC" or "KEGG"
pvalueCutoff = 0.05,
topn = 5,
add.gene = TRUE) #显示top5 GO term
head(enrich)
write.csv(enrich,"./ClusterGVis/GO_P0.05_500_cw.csv")

pdf('./ClusterGVis/GO_P0.05_cw.pdf', height = 20, width = 12, onefile = F)
visCluster(
object = cw,
plot.type = "both",
column_names_rot = 60,
markGenes.side = "left",
genes.gp = c('italic',fontsize = 13),
show_row_dend = F,
ht.col.list = list(col_range = c(-2, 0, 2),
col_color = c("#0da9ce", "white", "#e74a32")),
annoTerm.data = enrich,
go.size = "pval", #按p值显示注释大小
line.side = "left" #将表达趋势折线图放到左侧
)
dev.off()

最后一张图报错：

visCluster(

• object = cw,
• plot.type = "both",
• column_names_rot = 60,
• markGenes.side = "left",
• genes.gp = c('italic',fontsize = 13),
• show_row_dend = F,
• ht.col.list = list(col_range = c(-2, 0, 2),

•                  col_color =  c("#0da9ce", "white", "#e74a32")),
  

• annoTerm.data = enrich,
• go.size = "pval", #按p值显示注释大小
• line.side = "left" #将表达趋势折线图放到左侧
• )
  This palatte have 20 colors!
  No more than 4 columns!
  Error: names of text should have overlap to levels in align_to.
  In addition: Warning message:
  Unknown or uninitialised column: size.

[elegantmedstu]

当绘制kegg时报错，绘制go时无问题。
报错是：This palatte have 20 colors!
No more than 4 columns!
Error: names of text should have overlap to levels in align_to.
错误似乎出现在参数plot.type = "both"，当单纯绘制线图或者热图时没有出现报错

enrich <- enrichCluster(object = ck,
OrgDb = org.Hs.eg.db,
organism = 'hsa',
topn = 3,
add.gene = T, # whether return genes for output, default FALSE.
type = "KEGG", # which type to choose for enrichment "BP","MF","CC","KEGG" or "ownSet".
pvalueCutoff = 0.05,
seed = 5201314)
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Warning messages:
1: In clusterProfiler::bitr(tmp$gene, fromType = fromType, toType = toType, :
43.72% of input gene IDs are fail to map...
2: In clusterProfiler::bitr(tmp$gene, fromType = fromType, toType = toType, :
30.16% of input gene IDs are fail to map...
3: In clusterProfiler::bitr(tmp$gene, fromType = fromType, toType = toType, :
32.4% of input gene IDs are fail to map...
4: In clusterProfiler::bitr(tmp$gene, fromType = fromType, toType = toType, :
37.24% of input gene IDs are fail to map...
5: In clusterProfiler::bitr(tmp$gene, fromType = fromType, toType = toType, :
33.84% of input gene IDs are fail to map...
6: In clusterProfiler::bitr(tmp$gene, fromType = fromType, toType = toType, :
34.11% of input gene IDs are fail to map...
7: In clusterProfiler::bitr(tmp$gene, fromType = fromType, toType = toType, :
37.57% of input gene IDs are fail to map...
8: In clusterProfiler::bitr(tmp$gene, fromType = fromType, toType = toType, :
32.42% of input gene IDs are fail to map...

visCluster(object = ck,
plot.type = "both", # the plot type to choose which incuding "line","heatmap" and "both".
column_names_rot = 45,
markGenes = markGenes,
annoTerm.data = enrich,
go.size = 10,
#go.size = "pval", #按P值调整字体大小
line.side = "left", # 通路富集的注释连接与折线图的右边似乎并不太恰当
show_row_dend = F, # 不显示聚类树
term.text.limit = c(8,18))
This palatte have 20 colors!
No more than 4 columns!
Error: names of text should have overlap to levels in align_to.

[elegantmedstu]

问题出现在dd.gene = T，当设置为T时返回第5行，引起报错
enrichCluster(object = ck,
OrgDb = org.Hs.eg.db,
organism = 'hsa',
topn = 3,
add.gene = T, # whether return genes for output, default FALSE.
type = "KEGG", # which type to choose for enrichment "BP","MF","CC","KEGG" or "ownSet".
pvalueCutoff = 0.05,
seed = 5201314)

一个解决方法是：visCluster(object = ck,plot.type = "both",column_names_rot = 45,markGenes = markGenes,annoTerm.data = enrich[,1:4])

[junjunlab]

富集结果不能超过四列数据，可以自己处理一下

[Taoli0113]

富集结果不能超过四列数据，可以自己处理一下

好的好的，谢谢junjun老师！