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openbiox / UCSCXenaShiny

📊 An R package for interactively exploring UCSC Xena https://xenabrowser.net/datapages/; Book: https://lishensuo.github.io/UCSCXenaShiny_Book; App online: https://shiny.hiplot.cn/ucsc-xena-shiny/, https://shiny.zhoulab.ac.cn/UCSCXenaShiny
https://openbiox.github.io/UCSCXenaShiny/
GNU General Public License v3.0
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`tcga_surv_get` function for methylation profiles is failing in R studio #359

Open quiquemedina opened 1 day ago

quiquemedina commented 1 day ago

Dear developers,

I noticed that the function tcga_surv_get for “methylation” profiles is failing in R Studio (UCSCXenaShiny versions 2.1.0 and 2.2.0) (see print screen 1), as well as in the new online app (https://shiny.hiplot.cn/ucsc-xena-shiny/). The failure does not seem to be an issue with URL connectivity, as the function works fine in both the older UCSCXenaTools version 1.4.8 and the previous online app (https://shixiangwang.shinyapps.io/ucscxenashiny/).

Here is the code using UCSCXenaShiny versions 2.1.0 and 2.2.0: r Copiar código library(UCSCXenaShiny) library(UCSCXenaTools) library(survminer)

data <- tcga_surv_get( item = "(PAX9 + SEMA4A)", TCGA_cohort = "LUAD", profile = "methylation", TCGA_cli_data = dplyr::full_join(load_data("tcga_clinical"), load_data("tcga_surv"), by = "sample"), opt_pancan = .opt_pancan )

tcga_surv_plot( data, time = "DSS.time", status = "DSS", cutoff_mode = "Custom", cutpoint = c(50, 50), profile = "methylation", palette = "aaas" ) Printscreen_1

image

image

However, using UCSCXenaTools version 1.4.8, the function works fine (Printscreen_2) r Copiar código library(UCSCXenaShiny) library(UCSCXenaTools) library(survminer)

data <- tcga_surv_get( item = "(PAX9 + SEMA4A)", TCGA_cohort = "LUAD", profile = "methylation", TCGA_cli_data = dplyr::full_join(load_data("tcga_clinical"), load_data("tcga_surv"), by = "sample") )

tcga_surv_plot( data, time = "DSS.time", status = "DSS", cutoff_mode = "Custom", cutpoint = c(50, 50), profile = "methylation", palette = "aaas" )

Printscreen_2

image

It seems that the code has not been updated for RStudio users after the UCSCXenaShiny versions 2.1.0 update.

Best regards,

Enrique

ShixiangWang commented 19 hours ago

@lishensuo

lishensuo commented 15 hours ago

Thank you for pointing out the issue. We've identified the cause of the bugs. The methylation datasets used in UCSCXenaShiny V2 were sourced from the GDC hub on the UCSC Xena platform:

Unfortunately, these datasets are currently inaccessible, which caused the error you encountered. We have now switched to alternative methylation datasets used in our V1 version. You should be able to run the methylation analysis successfully with the latest development version.