zhanghao-njmu / SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

Home Page:https://zhanghao-njmu.github.io/SCP/

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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'
)