Problems in using FeatureHeatmap

[zhangdae]

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

[zhanghao-njmu]

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'
)