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	Temporarily remove DisGeNET integration
Supplying the custom background results in internal server errors on the DisGeNET backend. We don't want to present results without a proper background set.
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					 3 changed files with 0 additions and 51 deletions
				
			
		|  | @ -19,7 +19,6 @@ RoxygenNote: 7.2.0 | ||||||
| Imports: | Imports: | ||||||
|     bslib, |     bslib, | ||||||
|     data.table, |     data.table, | ||||||
|     disgenet2r, |  | ||||||
|     DT, |     DT, | ||||||
|     geposan, |     geposan, | ||||||
|     glue, |     glue, | ||||||
|  |  | ||||||
							
								
								
									
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								R/server.R
									
										
									
									
									
								
							|  | @ -267,48 +267,5 @@ server <- function(options) { | ||||||
|         digits = 1 |         digits = 1 | ||||||
|       ) |       ) | ||||||
|     }) |     }) | ||||||
| 
 |  | ||||||
|     output$disgenet <- DT::renderDT({ |  | ||||||
|       withProgress( |  | ||||||
|         message = "Querying DisGeNET", |  | ||||||
|         value = 0.0, |  | ||||||
|         { # nolint |  | ||||||
|           setProgress(0.2) |  | ||||||
| 
 |  | ||||||
|           all_gene_names <- unique(results()[name != "", name]) |  | ||||||
|           filtered_gene_names <- unique(results_filtered()[name != "", name]) |  | ||||||
| 
 |  | ||||||
|           diseases <- suppressMessages( |  | ||||||
|             disgenet2r::disease_enrichment( |  | ||||||
|               all_gene_names, |  | ||||||
|               custom_universe = list(filtered_gene_names) |  | ||||||
|             ) |  | ||||||
|           ) |  | ||||||
| 
 |  | ||||||
|           data <- data.table(diseases@qresult) |  | ||||||
| 
 |  | ||||||
|           data <- data[, .(Description, Ratio, BgRatio, pvalue)] |  | ||||||
|           setorder(data, pvalue) |  | ||||||
| 
 |  | ||||||
|           dt <- DT::datatable( |  | ||||||
|             data, |  | ||||||
|             rownames = FALSE, |  | ||||||
|             colnames = c( |  | ||||||
|               "Disease", |  | ||||||
|               "Query ratio", |  | ||||||
|               "Total ratio", |  | ||||||
|               "p-value" |  | ||||||
|             ), |  | ||||||
|             options = list( |  | ||||||
|               pageLength = 25 |  | ||||||
|             ) |  | ||||||
|           ) |  | ||||||
| 
 |  | ||||||
|           dt <- DT::formatRound(dt, "pvalue", digits = 4) |  | ||||||
| 
 |  | ||||||
|           dt |  | ||||||
|         } |  | ||||||
|       ) |  | ||||||
|     }) |  | ||||||
|   } |   } | ||||||
| } | } | ||||||
|  |  | ||||||
							
								
								
									
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								R/ui.R
									
										
									
									
									
								
							|  | @ -101,13 +101,6 @@ ui <- function(options) { | ||||||
|                   style = "margin-top: 16px", |                   style = "margin-top: 16px", | ||||||
|                   DT::DTOutput("gost_details") |                   DT::DTOutput("gost_details") | ||||||
|                 ) |                 ) | ||||||
|               ), |  | ||||||
|               tabPanel( |  | ||||||
|                 title = "DisGeNET", |  | ||||||
|                 div( |  | ||||||
|                   style = "margin-top: 16px", |  | ||||||
|                   DT::DTOutput("disgenet") |  | ||||||
|                 ) |  | ||||||
|               ) |               ) | ||||||
|             ) |             ) | ||||||
|           ) |           ) | ||||||
|  |  | ||||||
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