Merge pull request #52 from ImmuneDynamics/development

Fixes to spatial analysis functions

DESCRIPTION

@@ -1,14 +1,15 @@
 Package: Spectre
 Type: Package
 Title: A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data. 
-Version: 0.5.0
+Version: 0.5.1
 Author: Thomas Ashhurst, Felix Marsh-Wakefield, Givanna Putri
 Maintainer: Thomas Ashhurst <thomas.ashhurst@sydney.edu.au>
-Description: A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry data. 
+Description: A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data. 
 Depends: R (>= 3.6.0)
 License: MIT Licence
 Encoding: UTF-8
 LazyData: true
+biocViews:
 Imports:
     devtools,
     plyr,
@@ -46,7 +47,11 @@ Imports:
     sf,
     stars,
     qs,
+    s2,
     exactextractr
+    flowCore,
+    Biobase,
+    flowViz,
 Suggests:
 RoxygenNote: 7.1.1
 Roxygen: list(markdown = TRUE)

R/do.create.outlines.R

@@ -32,6 +32,10 @@ do.create.outlines <- function(spatial.dat,
 
       if(method == 'stars'){
         message(paste0("Creating polygons, outlines, and centroids using 'stars' method."))
+        require(stars)
+        require(sf)
+        require(sp)
+        require(s2)
       }
 
       if(method == 'raster'){
@@ -53,13 +57,13 @@ do.create.outlines <- function(spatial.dat,
 
         mask <- spatial.dat[[i]]$MASKS[[mask.name]]$maskraster
 
-        message(paste0("Processing masks for ROI ", i))
+        message(paste0("  -- Processing masks for ROI ", i))
 
         ## rasterToPolygons method
             if(method == 'raster'){
               polygon <- rasterToPolygons(mask, dissolve=TRUE) # This is the long step
               spatial.dat[[i]]$MASKS[[mask.name]][["polygons"]] <- polygon
-              message("... polygons complete")
+              message("    ... polygons complete")
             }
 
         ## stars method
@@ -68,16 +72,18 @@ do.create.outlines <- function(spatial.dat,
               require(stars)
               require(sf)
               require(sp)
+              require(s2)
 
               names(mask) <- "TEMP_MASK"
 
               stars.mask <- stars::st_as_stars(mask)
 
-              sf::st_crs(stars.mask) <- 4326
+              #sf::st_crs(stars.mask) <- 4326
 
               res <- sf::st_as_sf(stars.mask, # requires the sf, sp, raster and stars packages
                                   as_points = FALSE,
                                   merge = TRUE) #,
+
                                   #na.rm = TRUE)
                                   #group = TRUE) # TRUE crashes, FALSE does not
 
@@ -94,18 +100,20 @@ do.create.outlines <- function(spatial.dat,
               crs(polygon) <- NA
 
               spatial.dat[[i]]$MASKS[[mask.name]][["polygons"]] <- polygon
-              message("... polygons complete")
+              message("     ... polygons complete")
             }
 
     ### Create outlines
-        outline <- fortify(polygon)
+        suppressMessages(
+          outline <- fortify(polygon)
+        )
         spatial.dat[[i]]$MASKS[[mask.name]][["outlines"]] <- outline
-        message("... outlines complete")
+        message("     ... outlines complete")
 
     ### Create centroids
         centroids <- gCentroid(polygon,byid=TRUE)
         spatial.dat[[i]]$MASKS[[mask.name]][["centroids"]] <- centroids
-        message("... centroids complete")
+        message("     ... centroids complete")
       }
 
   message("Returning spatial data")

R/make.colour.plot.R

@@ -364,17 +364,41 @@ make.colour.plot <- function(dat,
 
       if(col.type == "continuous"){
         p <- p + theme(panel.background = element_rect(fill = "white", colour = "black", size = 0.5), # change 'colour' to black for informative axis
-                       axis.title.x=element_text(color="Black", face="bold", size=18),
-                       axis.title.y=element_text(color="Black", face="bold", size=18),
-                       plot.title = element_text(color="Black", face="bold", size=22, hjust=0) # size 70 for large, # 18 for small
+                       axis.title.x=element_text(color="Black", 
+                                                 #face="bold", 
+                                                 size=28),
+
+                       axis.title.y=element_text(color="Black", 
+                                                 #face="bold", 
+                                                 size=28),
+
+                       # axis.ticks = element_line(size = 4),
+                       # axis.line = element_line(size = 1),
+                       axis.text.x = element_text(color="Black", size=24),
+                       axis.text.y = element_text(color="Black", size=24), 
+                       panel.border = element_rect(colour = "black", fill = NA, size = 2),
+
+                       plot.title = element_text(color="Black", face="bold", size=32, hjust=0) # size 70 for large, # 18 for small
         )
       }
 
       if(col.type == "factor"){
         p <- p + theme(panel.background = element_rect(fill = "white", colour = "black", size = 0.5),
-                       axis.title.x=element_text(color="Black", face="bold", size=18),
-                       axis.title.y=element_text(color="Black", face="bold", size=18),
-                       plot.title = element_text(color="Black", face="bold", size=22, hjust=0) # size 70 for large, # 18 for small
+                       axis.title.x=element_text(color="Black", 
+                                                 #face="bold", 
+                                                 size=28),
+
+                       axis.title.y=element_text(color="Black", 
+                                                 #face="bold", 
+                                                 size=28),
+
+                       # axis.ticks = element_line(size = 4),
+                       # axis.line = element_line(size = 1),
+                       axis.text.x = element_text(color="Black", size=24),
+                       axis.text.y = element_text(color="Black", size=24), 
+                       panel.border = element_rect(colour = "black", fill = NA, size = 2),
+
+                       plot.title = element_text(color="Black", face="bold", size=32, hjust=0) # size 70 for large, # 18 for small
         )
 
         #p <- p + theme(legend.position="bottom")
@@ -392,7 +416,7 @@ make.colour.plot <- function(dat,
                        legend.position=legend.loc,
                        #legend.key.height=unit(0.7,"cm"),
                        #legend.key.width=unit(0.7,"cm"),
-                       legend.text=element_text(size=12), # large = 30 # small = 8
+                       legend.text=element_text(size=18), # large = 30 # small = 8
                        legend.title=element_blank()
                        )
       }
@@ -403,7 +427,7 @@ make.colour.plot <- function(dat,
                        legend.position=legend.loc,
                        #legend.key.height=unit(1,"cm"), # large = 3 # small = 1.2
                        #legend.key.width=unit(0.7,"cm"), # large = 1 # small = 0.4
-                       legend.text=element_text(size=12), # large = 30 # small = 8
+                       legend.text=element_text(size=18), # large = 30 # small = 8
                        legend.title=element_blank()
                        )  
       }

R/read.spatial.files.R

@@ -29,21 +29,36 @@ read.spatial.files <- function(rois,
   ### Packages
 
       require('raster')
-  
+
   ### Checks
 
       if(multi.tiff == TRUE){
-        if(length(grep(".tif", rois)) != length(rois)){
+        if(length(grep(ext, rois)) != length(rois)){
           stop("It appears that your list of ROIs are not TIFF stack files, and might be directories full of single TIFFs (i.e. one TIFF per channel. If this is correct, please use 'multi.tiff = FALSE'")
         }
       }
+
+      setwd(roi.loc)
+      setwd(i)
+      tiffs <- list.files(pattern = ext)
+
+      # https://stackoverflow.com/questions/7963898/extracting-the-last-n-characters-from-a-string-in-r
+      substrRight <- function(x, n){
+        substr(x, nchar(x)-n+1, nchar(x))
+      }
+
+      if(ext != substrRight(tiffs[1],nchar(ext))){
+        message(paste0("Error: Your extension '", ext, "' does not match the extensions of your TIF or TIFF files"))
+        stop(paste0("Example file name: ", tiffs[1]), call. = FALSE)
+      }
+
+      rm(tiffs)
 
   ### Setup
-
-      # message("This is a developmental Spectre-spatial function that is still in testing phase with limited documentation. We recommend only using this function if you know what you are doing.")
+      
+      setwd(roi.loc)
       ROI.list <- list()
       spatial.dat <- list()
-      setwd(roi.loc)
 
   ### Loop for ROIs -- one TIFF per ROI (i.e. tiff stack)
 
@@ -83,7 +98,7 @@ read.spatial.files <- function(rois,
           setwd(roi.loc)
           setwd(i)
           tiffs <- list.files(pattern = ext)
-
+          
           ## TIFF loop
           active.roi <- list()
 

README.md

@@ -5,7 +5,7 @@ A computational toolkit in R for the integration, exploration, and analysis of h
 <img src="https://raw.githubusercontent.com/tomashhurst/tomashhurst.github.io/master/images/Spectre.png">
 
 ### Current version
-`v0.5.0`
+`v0.5.1`
 
 ### About
 

segmentation/Modified bodenmiller segmentation/1_panel/panel.csv

@@ -0,0 +1,14 @@
+Metal Tag,Target,full,ilastik,ilastik_order
+Pr141,Alpha_SMA,1,0,
+Nd143,Vimentin,1,0,
+Sm149,CD11b,1,1,1
+Sm152,CD45,1,1,2
+Gd156,CD45,1,1,3
+Tb159,CD68,1,1,4
+Dy161,CD20,1,1,5
+Dy162,CD8a,1,1,6
+Tm169,Collagen_I,1,0,
+Er170,CD3,1,1,7
+Yb176,HH3,1,1,8
+Ir191,DNA-1,1,1,9
+Ir193,DNA-2,1,1,10

segmentation/Modified bodenmiller segmentation/1_panel/panel_template.csv

@@ -0,0 +1,42 @@
+Metal Tag,Target,full,ilastik,order
+Pd104,,1,,
+In113,,1,,
+In115,,1,,
+Pr141,,1,,
+Nd142,,1,,
+Nd143,,1,,
+Nd144,,1,,
+Nd145,,1,,
+Nd146,,1,,
+Sm147,,1,,
+Nd148,,1,,
+Sm149,,1,,
+Nd150,,1,,
+Eu151,,1,,
+Sm152,,1,,
+Eu153,,1,,
+Sm154,,1,,
+Gd155,,1,,
+Gd156,,1,,
+Gd158,,1,,
+Tb159,,1,,
+Gd160,,1,,
+Dy161,,1,,
+Dy162,,1,,
+Dy163,,1,,
+Dy164,,1,,
+Ho165,,1,,
+Er166,,1,,
+Er167,,1,,
+Er168,,1,,
+Tm169,,1,,
+Er170,,1,,
+Yb171,,1,,
+Yb172,,1,,
+Yb173,,1,,
+Yb174,,1,,
+Lu175,,1,,
+Yb176,,1,,
+Ir191,DNA1,1,,
+Ir193,DNA2,1,,
+Bi209,,1,,