manifest + css

almaan · Jun 18, 2020 · be65605 · be65605
1 parent 0c28625
commit be65605
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Showing 15 changed files with 727 additions and 329 deletions.
diff --git a/app/app.R b/app/app.R
@@ -2,48 +2,50 @@ library(ggplot2)
 library(jpeg)
 library(Matrix)
 library(grid)
-library(shiny)
 library(magrittr)
-library(shinycssloaders)
-library(shinydashboard)
 library(magick)
 library(zeallot)
-library(shinyWidgets)
 library(yaml)
 
+library(shiny)
+library(shinyWidgets)
+library(shinycssloaders)
+library(shinydashboard)
+
+
 source("utils.R")
 
 CONFIG <- read_yaml("config.yaml")
 PATIENTS <- names(CONFIG)
-N.PATIENTS <- length(PATIENTS)
 
 
 #### pre-run setup ####
 
 theme_empty <- make_empty_theme()
 
-dims.list <- readRDS("data/dims.list")
-imdims.list <- readRDS("data/imdims.list")
 var.features.list <- readRDS("data/var.features.list")
+imdims.list <- readRDS("data/imdims.list")
+dims.list <- readRDS("data/dims.list")
 data.list <- readRDS("data/data.list")
-sc.list <- readRDS("data/cs.list")
-scs <- Reduce(intersect, lapply(sc.list, colnames))
-
-t1.list <- readRDS("data/t1.list")
-t1.cells <- Reduce(intersect,
- lapply(t1.list,
- function(x){colnames(x[[1]])}))
-
-t2.list <- readRDS("data/t2.list")
-t2.cells <- Reduce(intersect,
- lapply(t2.list,
- function(x){colnames(x[[1]])}))
-
-t3.list <- readRDS("data/t3.list")
-t3.cells <- Reduce(intersect,
- lapply(t3.list,
- function(x){colnames(x[[1]])}))
 
+sc.list <- readRDS("data/cs.list")
+scs <- Reduce(intersect, lapply(sc.list,
+ colnames))
+
+c(t1.list,
+ t2.list,
+ t3.list) %<-% lapply(1:3,
+ function(x) {readRDS(file.path("data",
+ paste0("t",
+ x,
+ ".list")))})
+
+c(t1.cells,
+ t2.cells,
+ t3.cells) %<-% lapply(list(t1.list,t2.list,t3.list),
+ function(x){Reduce(intersect,
+ lapply(x,colnames))}
+ )
 
 #### UI ####
 ui <- dashboardPage(
@@ -119,8 +121,6 @@ ui <- dashboardPage(
  )
 )
 
-
-
 ### SERVER ####
 server <- function(input, output, session) {
 
@@ -246,14 +246,18 @@ server <- function(input, output, session) {
  size = session$clientData$output_Aplot1_width/150,
  alpha = input$alpha,
  shape = 21) +
- theme_empty +
 
- labs(title = ifelse(rv$lastBtn %in% c("t1", "t2", "t3"), paste0("Cell type: ", variable),
- paste0("Gene: ", variable)),
+ theme_empty +
+
+ ggtitle(ifelse(rv$lastBtn %in% c("t1", "t2", "t3"),
+ paste0("Cell type: ", variable),
+ paste0("Gene: ", variable))) +
+
+ labs(fill = ifelse(rv$lastBtn %in% c("t1", "t2", "t3"),
+ "Cell type \nproportion",
+ "Expression\n(Normalized)")
+ ) +
 
- fill = ifelse(rv$lastBtn %in% c("t1", "t2", "t3"),
- "Cell type \nproportion",
- "Gene Expression\n(Normalized)")) +
 
  scale_x_continuous(limits = c(0, dims[[i]][1]), expand = c(0, 0)) +
  scale_y_continuous(limits = c(0, dims[[i]][2]), expand = c(0, 0)) +

diff --git a/app/data/t1.list b/app/data/t1.list
diff --git a/app/data/t2.list b/app/data/t2.list
diff --git a/app/data/t3.list b/app/data/t3.list
diff --git a/app/data_backup/cs.list b/app/data_backup/cs.list
diff --git a/app/data_backup/data.list b/app/data_backup/data.list
diff --git a/app/data_backup/dims.list b/app/data_backup/dims.list
diff --git a/app/data_backup/imdims.list b/app/data_backup/imdims.list
diff --git a/app/data_backup/t1.list b/app/data_backup/t1.list
diff --git a/app/data_backup/t2.list b/app/data_backup/t2.list
diff --git a/app/data_backup/t3.list b/app/data_backup/t3.list
diff --git a/app/data_backup/var.features.list b/app/data_backup/var.features.list