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How many database can we chose in function 'FeatureHeatmap(db = )'

Open zhangdae opened this issue 1 year ago • 4 comments

I want to use this command to finifsh function enrichment,using hallmark dataset,but whatever I write ,always report an error. I tried h/H/hallmark,always report thee error.

  •    ht2 <- FeatureHeatmap(srt = scrun,features = de_g$gene,feature_split = de_g$group1,group.by = 'RNA_snn_res.1.1',
                     species = 'Homo_sapiens',db = 'HallMark',anno_terms = TRUE,anno_keys = T,mirror = 'asia',use_raster = F)
    

[2023-09-01 01:16:08] Start Enrichment Workers: 125 Species: Homo_sapiens Permform enrichment... |=====================================================================================================| 100%

Error: BiocParallel errors 26 remote errors, element index: 1, 2, 3, 4, 5, 6, ... 0 unevaluated and other errors first remote error: Error in base::rowSums(x, na.rm = na.rm, dims = dims, ...): 'x' must be an array of at least two dimensions

zhangdae avatar Aug 31 '23 17:08 zhangdae

The source code is tooo complicated to me,I can`t find how many database could be used in this command :-(, besides GO_BP/MF/CC,KEGG,wikipathway.

zhangdae avatar Aug 31 '23 17:08 zhangdae

The code I attch can perfectly run when chosing db = GO_BP/MF/CC,KEGG,wikipathway

zhangdae avatar Aug 31 '23 17:08 zhangdae

Apologies, the documentation for the SCP functions is still being written. To discover the available database names within the SCP package, please refer to the documentation of PrepareDB function.

zhanghao-njmu avatar Sep 01 '23 02:09 zhanghao-njmu

Thanks for replying

zhangdae avatar Sep 02 '23 09:09 zhangdae