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R/Palettes.R

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+col_cluster <- list()
+col_cluster[["SubType_Layer"]] <- c(
+  "L2/3 IT" = '#ffda11', "L4/5 IT" = '#f68d45', "L5 IT" = '#26d5ff', "L6 IT" = '#f05a9e', 
+  "L5 PT" = '#6d92ff', "L5 NP" = '#8976ff', "L6 CT" = '#e01fff',
+  'Pvalb' = '#c48983', 'Sst' = '#c7b766', 'Vip' = '#0092b6', 'Lamp5' = '#a9d166',
+  "Astro" = '#d08fbe', "Endo" = '#bb7967', "Microglia" = '#00a7cf', "Oligo" = '#5e45a6',
+  "OPC" = '#1470d6')
+col_cluster[["SubType"]] <- c(
+  "L2/3_IT_1"='#ffd600', "L2/3_IT_2"='#ffff8d',
+  "L4/5_IT_1"='#ff6d00',  "L4/5_IT_2"='#ffd180',
+  "L5_IT_1"='#0091ea', "L5_IT_2"='#80d8ff',
+  "L6_IT_1"='#c51162', "L6_IT_2"='#ff80ab',
+  "L5_PT_1"='#304ffe', "L5_PT_2"='#8c9eff',
+  "L5_NP"='#8976ff',
+  "L6_CT_1"='#f05a9e', "L6_CT_2"="#d75ff6")
+
+col_sample <- c('Adult1' = "#1e76b2", 'Adult2' = "#fd7e0c", 'Adult3' = "#2a9c67")
+
+col_Glu_GABA <- c('Excitatory' = "#7570B3FF", 'Inhibitory' = "#E7298AFF",
+                  'Non-neuron' = "#66A61EFF")
+
+col_MainType <- c('Excitatory' = "#7570B3FF", 'Inhibitory' = "#E7298AFF",
+                  'Astro' = "#d08fbe", 'Endo' = "#bb7967", 'Microglia' = "#00a7cf",
+                  'Oligo' = "#5e45a6", 'OPC' = "#1470d6")
+
+
+
+col_BC_label <- c(Barcoded = '#f8cb7f', Unbarcoded = '#90a5e1')
+
+col_Barcode <- c(
+  'VIS-I'="#536dfe",'CP-I'="#448aff",'SSp-I'="#40c4ff",'AUD-I'="#18ffff",'RSP-I'="#84ffff",
+  'ACB-I'="#ff6e40",'BLA-I'="#ffab40",'ENTl-I'="#ffd740",'AId-I'="#ffff00",'ECT-I'="#ffff8d",
+  'CP-C'="#00bfa5",'PL-C'="#00c853",'RSP-C'="#64dd17",
+  'ACB-C'="#a7ffeb",'BLA-C'="#b9f6ca",'ENTl-C'="#ccff90",'AId-C'="#b2ff59",'ECT-C'="#69f0ae",
+  'MD-I'="#ff5252",'LHA-I'="#ff4081",'SC-I'="#e040fb",'DR-I'="#ff8a80",'RE-I'="#ff80ab",'VTA-I'="#ea80fc",
+  'none'="lightgray")
+
+col_BC_num <- c('#5e4fa2','#3288bd','#66c2a5','#abdda4','#e6f598','#fee08b','#fdae61',
+                '#f46d43','#d53e4f','#9e0142')
+
+col_Proj_module <- c('ITi-D'='#1f77b4', 'ITi-V'='#ff7f0e','ITc'='#2ca02c','PTi'='#d62728')
+col_Proj_subtype <- c(
+  "1"="#304ffe","14"="#3d5afe","17"="#536dfe","22"="#8c9eff","23"="#2962ff","25"="#2979ff",
+  "26"="#448aff","27"="#82b1ff","28"="#80d8ff","29"="#0091ea","31"="#00b0ff",
+  "7"="#dd2c00","8"="#ff3d00","9"="#ff6e40","10"="#ff9e80","15"="#ff6d00","16"="#ff9100",
+  "18"="#ffab40","19"="#ffd180","20"="#ffab00","21"="#ffc400",
+  "2"="#00c853","3"="#00e676","11"="#69f0ae","12"="#b9f6ca","13"="#64dd17","24"="#76ff03",
+  "30"="#b2ff59","32"="#ccff90","33"="#aeea00",
+  "4"="#d50000","5"="#ff8a80","6"="#f50057")
+
+col_Proj_ITPT <- c('IT'='#1f77b4', 'PT'='#d62728')
+col_D_V <- c('Dorsal'='#1f77b4', 'Ventral'='#ff7f0e')
+

R/allenAnnotationsFunctions.R

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+#------------------ Librairies ------------------  
+library(rjson)
+
+
+
+#------------------ Ontology handling ------------------ 
+
+get.id.from.acronym <- function(acronym){
+  
+  rec.func <- function(acronym, json){
+    
+    if(is.null(json))
+      return()
+    
+    if(acronym == json$acronym)
+      return(json$id)
+    
+    return(unlist(lapply(json$children, function(x){return(rec.func(acronym, x))})))
+  }
+  
+  #Loading json data
+  json_data <- fromJSON(file= paste(path.matrices,'ontology.json',sep='/'))
+  json <- json_data$msg[[1]]
+  
+  return(rec.func(acronym, json))
+}
+
+
+
+#------------------ 3D handling ------------------ 
+
+mesh3d.allen.annot.from.id <- function(id, max.nrows = 349696, bregma = c(5200, 650, 5700)/1000, no.normals = F){ #5400, 650, 5700 In mm, AP/DV/ML
+  
+  fpath <- sprintf('%s/%d.obj', allen.annot.path, id)
+  
+  vert.start <- 0
+  vert.end <- 0
+  norm.start <- 0
+  norm.end <- 0
+  face.start <- 0
+  face.end <- 0
+  i <- 0
+  
+  con <- file(fpath, 'r')
+  while(TRUE){
+    
+    i <- i + 1
+    line = readLines(con, n = 1)
+    
+    if (length(line) == 0)
+      break
+    
+    if(startsWith(line, 'v ') & vert.start == 0)
+      vert.start <- i
+    
+    if(vert.start != 0 & vert.end == 0 & !startsWith(line, 'v '))
+      vert.end <- i
+    
+    if(startsWith(line, 'vn') & norm.start == 0)
+      norm.start <- i
+    
+    if(norm.start !=0 & norm.end == 0 & !startsWith(line, 'vn'))
+      norm.end <- i
+    
+    if(startsWith(line, 'f') & face.start == 0)
+      face.start <- i
+    
+    if(face.start !=0 & face.end == 0 & !startsWith(line, 'f'))
+      face.end <- i
+    
+  }
+  
+  if(face.end == 0)
+    face.end <- i - 1
+  
+  close(con)
+  
+  con <- file(fpath, 'r')
+  line = readLines(con, n = (vert.start - 1))
+  line = readLines(con, n = vert.end - vert.start)
+  vertices <- strsplit(line, ' ')
+  vertices.ul <- unlist(vertices)
+  df.vertices <- data.frame(x = as.numeric(vertices.ul[seq(from = 2, to = 4*length(vertices), by = 4)]),
+                            y = as.numeric(vertices.ul[seq(from = 3, to = 4*length(vertices), by = 4)]),
+                            z = as.numeric(vertices.ul[seq(from = 4, to = 4*length(vertices), by = 4)]))
+  close(con)
+  
+  con <- file(fpath, 'r')
+  line = readLines(con, n = (norm.start - 1))
+  line = readLines(con, n = norm.end - norm.start)
+  norm <- strsplit(line, ' ')
+  norm.ul <- unlist(vertices)
+  df.norm <-  data.frame(   x = as.numeric(norm.ul[seq(from = 2, to = 4*length(norm), by = 4)]),
+                            y = as.numeric(norm.ul[seq(from = 3, to = 4*length(norm), by = 4)]),
+                            z = as.numeric(norm.ul[seq(from = 4, to = 4*length(norm), by = 4)]))
+  close(con)
+  
+  con <- file(fpath, 'r')
+  line = readLines(con, n = (face.start - 1))
+  line = readLines(con, n = face.end - face.start)
+  face <- strsplit(line, ' ')
+  face <- lapply(face, function(x){return(unlist(strsplit(x, '//')))})
+  face.ul <- unlist(face)
+  
+  df.face <-  data.frame(   x = as.numeric(face.ul[seq(from = 2, to = 7*length(face), by = 7)]),
+                            y = as.numeric(face.ul[seq(from = 4, to = 7*length(face), by = 7)]),
+                            z = as.numeric(face.ul[seq(from = 6, to = 7*length(face), by = 7)]))
+  close(con)
+  
+  if(!no.normals){
+    mesh <- tmesh3d(vertices = rbind(t(df.vertices),1),
+                    indices = t(df.face),
+                    normals = t(df.norm)[c(3,2,1),])
+  }else{
+    mesh <- tmesh3d(vertices = rbind(t(df.vertices),1),
+                    indices = t(df.face))
+  }
+  
+  mesh$vb[1:3,] <- mesh$vb[1:3,] / 1000 
+  
+  mesh$vb[1,] <- -mesh$vb[1,] + bregma[1]
+  mesh$vb[2,] <- -mesh$vb[2,] + 0.05 #Maybe not the +0.05
+  mesh$vb[3,] <- -mesh$vb[3,] + bregma[3]
+  
+  tmp <- mesh$vb[1,]  
+  mesh$vb[1,] <- mesh$vb[3,]
+  mesh$vb[3,] <- tmp
+  
+  return(mesh)
+  
+}
+
+
+
+mesh3d.show.outline <- function(col = 'lightgray', alpha = 0.1){
+  shade3d(mesh3d.allen.annot.from.id(get.id.from.acronym('root')), col = col, alpha = alpha)
+}
+
+mesh3d.new.window <- function(show.outline = TRUE){
+  
+  rgl.open()
+  rgl.bg(color = 'white')
+  par3d(windowRect = c(0, 0, 1920, 1080))
+  
+  if(show.outline)
+    mesh3d.show.outline()
+}
+
+
+
+

R/includes.R

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+library(rgl)
+#library(wholebrain)
+
+path.bin <- 'R/'
+path.matrices <-'data/3D_data/'
+allen.annot.path <- paste(path.matrices , 'allen-mesh', sep = '/')
+
+load(paste(path.matrices ,'atlasspots.RData',sep='/'))
+load(paste(path.matrices , 'vivid-colors.RData', sep='/'))
+
+source(paste(path.bin,'allenAnnotationsFunctions.R',sep='/'))