can't determine keyType automatically; need to set 'keyType' explicitly...

[Gavin098]

Hello,Dear Dr, When I run the data for non-model species following documents of CBNplot, some code cannot running successfully in Linux.

library(DESeq2)
library(clusterProfiler)
library(ggplot2)
library(CBNplot)
counts = read.table("rsem.merged.gene_counts_SDRE.tsv_round", header=1, row.names=1,sep=' ')
meta = sapply(colnames(counts), function (x) substring(x,1,2))
meta = data.frame(meta)
colnames(meta) = c("Condition")
dds <- DESeqDataSetFromMatrix(countData = counts,
                              colData = meta,
                              design= ~ Condition)
filt <- rowSums(counts(dds) < 10) > dim(meta)[1]*0.9
dds <- dds[!filt,]
## Perform DESeq2()
dds = DESeq(dds)
res = results(dds, pAdjustMethod = "bonferroni")
## apply variance stabilizing transformation
v = vst(dds, blind=FALSE)
vsted = assay(v)
pdf(file = "./PCA_DESeq2QC.pdf", width = 12, height = 9);
DESeq2::plotPCA(v, intgroup="Condition")+
    theme_bw()
dev.off()

sig = subset(res, padj<0.05)
cand.entrez = rownames(sig)
GO_anno <- read.csv("gene_go_annotation_from_ipr_nr.tab", sep = "\t",header = T,check.names = F)                               
GO_description <- read.csv("go_term.list", sep = "\t",header = T,check.names = F)                                              
KEGG_anno <- read.csv("kegg_gene.txt", sep = "\t",header = T,check.names = F)                                                  
KEGG_description <- read.csv("kegg_description.txt", sep = "\t", check.names = F, header = T)
#Go enrichment analysis
pwayGO <- clusterProfiler::enricher(cand.entrez,TERM2GENE=GO_anno,TERM2NAME=GO_description,pvalueCutoff = 0.05, pAdjustMethod = "BH")
## Store the similarity
pwayGO = enrichplot::pairwise_termsim(pwayGO)
## Define including samples
incSample = rownames(subset(meta, Condition=="SD"))
#plot
pdf(file = "./barplot_GO.pdf", width = 12, height = 9);
barplot(pwayGO, showCategory = 15)
dev.off()

pdf(file = "./bngeneplot_GO.pdf", width = 12, height = 9);
bngeneplot(results = pwayGO,
           exp = vsted,
           expSample = incSample,
           pathNum = 13, R = 50, showDir = T,
           convertSymbol = FALSE,
           strThresh = 0.7)
dev.off()

I have encountered problems as follows

> bngeneplot(results = pwayGO,
+            exp = vsted,
+            expSample = incSample,
+            pathNum = 13, R = 50, showDir = T,
+            convertSymbol = T,
+            expRow = "ENSEMBL",
+            strThresh = 0.7)
Error in setReadable(results, OrgDb = orgDb) : 
  can't determine keyType automatically; need to set 'keyType' explicitly...
> dev.off()
null device 
          1 

Good luck.