Comments (1)
Sometimes, it depends on your network and the Ensembl database itself (which may be inaccessible during their maintenance periods). You can try different mirror URLs or Ensembl versions, for example:
ht <- FeatureHeatmap(
srt = epi_sub, group.by = "sample.orig", features = DEGs$gene, feature_split = DEGs$group1,
species = "Homo_sapiens", db = c("GO_BP", "KEGG", "WikiPathway"), anno_terms = TRUE,
feature_annotation = c("TF", "SP"), feature_annotation_palcolor = list(c("gold", "steelblue"), c("forestgreen")),
height = 5, width = 4,
Ensembl_version = 105
# use the biomaRt::listEnsemblArchives() function to query the available database versions in Ensembl.
)
ht <- FeatureHeatmap(
srt = epi_sub, group.by = "sample.orig", features = DEGs$gene, feature_split = DEGs$group1,
species = "Homo_sapiens", db = c("GO_BP", "KEGG", "WikiPathway"), anno_terms = TRUE,
feature_annotation = c("TF", "SP"), feature_annotation_palcolor = list(c("gold", "steelblue"), c("forestgreen")),
height = 5, width = 4,
mirror = 'uswest'
# 'www', 'uswest', 'useast', 'asia'
)
from scp.
Related Issues (20)
- RunDEtest and FeatureHeatmap-enrichment take too long on my own dataset and can't run HOT 2
- 版本更新问题 HOT 3
- Error in t.default(srt@assays[[assay]]@data[intersect(cell_annotation, : 参数不是矩阵 HOT 1
- Package conflicts with dependencies HOT 1
- problem RunPAGA HOT 1
- Obtain associated p values for CellCorHeatmap
- Question about several functions in SCP HOT 1
- miniconda installation failed [exit code 2] HOT 2
- 关于Seurat版本更新后的使用问题 HOT 1
- Upgrade to work with Seurat5?
- Error in CellCorHeatmap()
- 一点点小建议
- Why is the number of DEGs output by FeatureHeatmap largely lower than that obtained from RunDEtest? HOT 1
- how to reduce run time for RunDynamicFeatures
- The angle parameter doesn't work in the theme function HOT 1
- Issue on installation: object ‘LayerData<-’ is not exported by 'namespace:SeuratObject' HOT 3
- Slingshot Warning HOT 4
- DynamicHeatmap issue HOT 2
- Spelling mistake in the GSEAPlot
- how to use Runharmony function in SCP ?
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