Error in depicting differential genesets while using irGSEA.bubble, irGSEA.bubble,irGSEA.barplot

chuiqin / irGSEA

The integration of single cell rank-based gene set enrichment analysis

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Error in depicting differential genesets while using irGSEA.bubble, irGSEA.bubble,irGSEA.barplot #9

Open sukyorsuki opened 2 years ago

sukyorsuki commented 2 years ago

irGSEA.heatmap.plot <- irGSEA.heatmap(object = result.dge,

method = "ssgsea",
top = 50,
show.geneset = NULL) Error in chr_as_locations(): ! Can't rename columns that don't exist. x Column p_val_adj doesn't exist. Run rlang::last_error() to see where the error occurred.

irGSEA.bubble.plot <- irGSEA.bubble(object = result.dge,

method = "ssgsea",
show.geneset = NULL,
top = 50) Error in chr_as_locations(): ! Can't rename columns that don't exist. x Column p_val_adj doesn't exist. Run rlang::last_error() to see where the error occurred.

ps, My 'result.dge' contains the p_val_adj

How to fix this error? THX

chuiqin commented 2 years ago

是的，这是一个BUG。这个BUG发生，是因为在执行irGSEA.score函数的时候，没有全选这4个方法("AUCell", "UCell", "singscore", "ssgsea")。然后，在执行irGSEA.bubble/irGSEA.bubble/irGSEA.barplot函数的时候，语句发生了错误 object[1:4] <- object[1:4] %>% purrr::map( ~.x %>% dplyr::rename(pvalue = p_val_adj))。我在新版本的irGSEA里面修复了这个BUG。在新版本的irGSEA中，即使在执行irGSEA.score函数的时候，我们没有全选这4个方法，也可以正常出图。

chuiqin commented 2 years ago

Yes, this is a bug. This bug occurs because the 4 methods ("AUCell", "UCell", "singscore", "ssgsea") are not selected when executing the irGSEA.score function. Then, when executing the irGSEA.bubble/irGSEA.bubble/irGSEA.barplot function, the statement has an error `object[1:4] <- object[1:4] %>% purrr::map( ~.x %>% dplyr::rename(pvalue = p_val_adj)). I fixed this bug in the new version of irGSEA. In the new version of irGSEA, even when we execute the irGSEA.score function, we can still draw pictures normally without selecting all the 4 methods.