homepage adjustment (#302)

* fix bug of download module * adjust homepage layout --------- Co-authored-by: Shixiang Wang (王诗翔) <[email protected]>
openbiox · Jan 21, 2024 · 030edc1 · 030edc1
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diff --git a/inst/rmd/report_template.Rmd b/inst/rmd/report_template.Rmd
@@ -1,6 +1,6 @@
 ---
-title: "Exploratory Analysis of UCSCXenashiny v2.0 Molecule Profiling"
-subtitle: "Summary Report for `r params$id_type` `r params$id_name`"
+title: "Exploratory Molecule Analysis of UCSCXenashiny v2.0"
+subtitle: "TCGA Pan-Cancer Report for `r params$id_type` `r params$id_name`"
 author: 
   - name: "Shensuo Li, UCSCXenashiny developer team"
     email: [email protected]
@@ -73,7 +73,7 @@ link_set = switch(id_type,
 
 
 # Introduction
-This report is generated using the results obtained from the `UCSCXenaShiny::mol_quick_analysis` function. The analysis encompasses 5 sections, each executed for `r id_type` ``r id_name`` sourced from the [dataset](`r link_set`) in UCSC Xena TOIL hub. [All TCGA projects](https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations) are analyzed individually and some cancer projects may be missing due to few samples with valid data for some analysis. The notation for statistical significance analysis is as follows: * indicates a P-value less than 0.05, ** indicates a P-value less than 0.01, and *** indicates a P-value less than 0.001. 
+This report is generated using the results obtained from the `UCSCXenaShiny::mol_quick_analysis` function. The analysis encompasses 5 sections, each executed for `r id_type` ``r id_name`` sourced from the [dataset](`r link_set`) in UCSC Xena TOIL(TCGA) hub. [All TCGA projects](https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations) are analyzed individually and some cancer projects may be missing due to few samples with valid data for some analysis. The notation for statistical significance analysis is as follows: * indicates a P-value less than 0.05, ** indicates a P-value less than 0.01, and *** indicates a P-value less than 0.001. 
 
 Please note that our [Shiny app](https://shiny.hiplot.cn/ucsc-xena-shiny/) offers more comprehensive exploration possibilities, including alternative datasets for the same molecule, alternative analysis methods, molecule-molecule analysis, personalized sample filtering and grouping, result visualization, and download options.
 

diff --git a/inst/shinyapp/App.R b/inst/shinyapp/App.R
@@ -85,6 +85,7 @@ pacman::p_load(
   shinyFeedback,
   shinythemes,
   shinyhelper,
+  shinycssloaders,
   survival,
   survminer,
   ezcox,
@@ -98,7 +99,8 @@ pacman::p_load(
   ggstatsplot,
   ggradar,
   zip,
-  msigdbr
+  msigdbr,
+  slickR
 )
 
 options(shiny.maxRequestSize=1024*1024^2)
@@ -415,18 +417,19 @@ ui <- tagList(
   autoWaiter(html = spin_loader(), color = transparent(0.5)), # change style https://shiny.john-coene.com/waiter/
   navbarPage(
     id = "navbar",
-    title = div(
-      img(src = "xena_shiny-logo_white.png", height = 49.6, style = "margin:-20px -15px -15px -15px")
-    ),
+    title = "UCSCXenaShiny v2",
+    # div(
+    #   img(src = "xena_shiny-logo_white.png", height = 49.6, style = "margin:-20px -15px -15px -15px")
+    # ),
     windowTitle = "UCSCXenaShiny",
     # inst/shinyapp/ui
     ui.page_home(),
     ui.page_repository(),
     ui.page_general_analysis(),
-    ui.page_pancan_tcga(),
-    ui.page_pancan_pcawg(),
-    ui.page_pancan_ccle(),
     ui.page_pancan_quick(),
+    ui.page_pancan_tcga(),
+    # ui.page_pancan_pcawg(),
+    # ui.page_pancan_ccle(),
     ui.page_download(),
     # ui.page_global(),
     ui.page_help(),

diff --git a/inst/shinyapp/helper/home_query.md b/inst/shinyapp/helper/home_query.md
@@ -0,0 +1 @@
+aaaaaaaaaaaaaa
diff --git a/inst/shinyapp/modules/function/modules-z-download-feat.R b/inst/shinyapp/modules/function/modules-z-download-feat.R
@@ -268,16 +268,16 @@ download_feat_Server = function(input, output, session, database = "toil",#id_op
 		output$x_axis_data_table = renderUI({
 			if(table.ui){
 				output$x_tmp_table = renderDataTable({
-					# shiny::validate(
-					# 	need(try(nrow(download_data())>0), 
-					# 		"No sample data were available. Please inspect operations in Preset step."),
-					# )
-					# if(check_numeric){
-					# 	shiny::validate(
-					# 		need(try(class(download_data()$value)!="character"), 
-					# 			"Please select a numeric variable."),
-					# 	)	
-					# }
+					shiny::validate(
+						need(try(nrow(download_data())>0), 
+							"No sample data were available. Please inspect operations in Preset step."),
+					)
+					if(check_numeric){
+						shiny::validate(
+							need(try(class(download_data()$value)!="character"), 
+								"Please select a numeric variable."),
+						)	
+					}
 					x_axis_data_ = download_data()[,c("Sample","value","cancer")]
 
 					if(class(x_axis_data_[,"value"])=="numeric"){