Problems in using FeatureHeatmap
zhangdae opened this issue · comments
When I use the function 'FeatureHeatmap',always failed to connect the dataset (hsapiens_gene_ensembl).Are there anyway to access this dataset locally?Or anyway to connect thee dataset.I recommened some of my friends this package,we all meet the same problem :-(
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
)
Error in curl::curl_fetch_memory(url, handle = handle) :
Timeout was reached: [feb2021.archive.ensembl.org:443] Operation timed out after 10006 milliseconds with 77102 bytes received
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'
)