Revert "Cibersort & mcpcounter"

DESCRIPTION

@@ -22,8 +22,7 @@ Imports:
     readr,
     shinycssloaders,
     wrapr,
-    forcats,
-    ggridges
+    forcats
 RoxygenNote: 7.0.2
 Suggests: 
     testthat (>= 2.1.0),

NAMESPACE

@@ -11,8 +11,6 @@ export(mod_explore_page_server)
 export(mod_explore_page_ui)
 export(mod_gene_variant_server)
 export(mod_gene_variant_ui)
-export(mod_immune_signatures_server)
-export(mod_immune_signatures_ui)
 export(mod_latent_variables_server)
 export(mod_latent_variables_ui)
 export(mod_resources_page_server)

R/mod_explore_page.R

@@ -18,7 +18,7 @@ mod_explore_page_ui <- function(id){
   tagList(
       dashboardPage(
         dashboardHeader(disable = T),
-        dashboardSidebar(sidebarMenu(
+        dashboardSidebar(
           id = "explorertabs",
           menuItem("Explore Home",
                    tabName = "dashboard",
@@ -27,7 +27,7 @@ mod_explore_page_ui <- function(id){
           menuItem("Analysis Modules",
                    icon = icon("chart-area"), startExpanded = TRUE,
                    menuSubItem(
-                     "Immune Cell Deconvolution",
+                     "Immune Infiltration",
                      tabName = "immune_infiltration",
                      icon = icon("cog")
                    ),
@@ -39,16 +39,15 @@ mod_explore_page_ui <- function(id){
                    menuSubItem(
                      "Latent Variables",
                      tabName = "latent_variables",
-                     icon = icon("cog"))))),
+                     icon = icon("cog")))),
         dashboardBody(
           tagList(
             tabItems(
               tabItem(
                 tabName = "dashboard"
                 ),
               tabItem(
-                tabName = 'immune_infiltration',
-                mod_immune_signatures_ui(ns("immune_signatures_ui_1"))
+                tabName = 'immune_infiltration'
                 ),
               tabItem(
                 tabName = "gene_var",
@@ -75,7 +74,6 @@ mod_explore_page_server <- function(input, output, session, specimens){
 
   callModule(mod_gene_variant_server, "gene_variant_ui", specimens)
   callModule(mod_latent_variables_server, "latent_variables_ui_1", specimens)  
-  callModule(mod_immune_signatures_server, "immune_signatures_ui_1", specimens)
 }
 
 ## To be copied in the UI

R/mod_latent_variables.R

@@ -51,8 +51,6 @@ mod_latent_variables_server <- function(input, output, session, specimens){
       dplyr::summarize(sdev = sd(value)) %>% 
     dplyr::top_n(10, sdev) 
 
-   validate(need(nrow(foo)>0, "No latent variable data found. Please modify your cohort."))
-
    foo2 <- dplyr::filter(kairos::latent_var,
                          latent_var %in% foo$latent_var) %>% 
      dplyr::mutate(latent_var = stringr::str_trunc(latent_var, 15)) %>%