@@ -69,6 +69,7 @@ importFrom(methods,validObject)

 importFrom(raster,as.raster)

 importFrom(stats,quantile)

 importFrom(tools,file_ext)

+importFrom(tools,file_path_sans_ext)

 importFrom(utils,packageVersion)

 importFrom(viridis,inferno)

 importFrom(viridis,viridis)

@@ -73,11 +73,11 @@ NULL

   # legend

   if(!("legend" %in% names(dotArgs))){

     legendparam <- list(colour_by.title.font = 1,

-                        colour_by.title.cex = 0.7,

+                        colour_by.title.cex = NULL,

                         colour_by.labels.cex = NULL,

                         colour_by.legend.cex = NULL,

                         outline_by.title.font = 1,

-                        outline_by.title.cex = 0.7,

+                        outline_by.title.cex = NULL,

                         outline_by.labels.cex = NULL,

                         outline_by.legend.cex = NULL,

                         margin = 2)

@@ -129,7 +129,7 @@ NULL

   if(!("display" %in% names(dotArgs))){

     dotArgs$display <- "all"

   } else {

-    if(is.character(dotArgs$display) ||

+    if(!is.character(dotArgs$display) ||

        !(dotArgs$display %in% c("all", "single"))){

       stop("Invalid 'display' entry.")

     }

@@ -357,7 +357,7 @@ NULL

                     "'colour_by.title.cex' should be a single number"))

       }

     } else {

-      legendparam$colour_by.title.cex <- 0.7

+      legendparam$colour_by.title.cex <- NULL

     }

     if("colour_by.labels.cex" %in% names(legendparam)){

@@ -401,7 +401,7 @@ NULL

                     "'outline_by.title.cex' should be a single number"))

       }

     } else {

-      legendparam$outline_by.title.cex <- 0.7

+      legendparam$outline_by.title.cex <- NULL

     }

     if("outline_by.labels.cex" %in% names(legendparam)){

@@ -298,6 +298,7 @@

 # Custom function to display images

 #' @importFrom S4Vectors SimpleList

 #' @importFrom EBImage Image

+#' @importFrom tools file_ext file_path_sans_ext

 #' @importFrom graphics par plot rasterImage strheight text

 #' @importFrom grDevices png jpeg tiff dev.off

 .displayImages <- function(object, image, exprs_values, outline_by,

@@ -346,7 +347,7 @@

     cur_out <- list()

   }

-  if(!is.null(plottingParam$save_image)){

+  if(!is.null(plottingParam$save_image) && plottingParam$display == "all"){

     image_location <- plottingParam$save_image$filename

     image_scale <- plottingParam$save_image$scale

     cur_ext <- file_ext(image_location)

@@ -371,7 +372,7 @@

       yaxs="i", xaxt="n", yaxt="n", col = "white")

   on.exit(par(cur_par))

-  if(plottingParam$display = "all"){

+  if(plottingParam$display == "all"){

     plot(x_len, y_len, type="n", xlab="", ylab="",

          asp = 1, ylim = rev(y_len))

   }

@@ -389,13 +390,44 @@

       ybottom <- i*m_height - (m_height - dim_y)/2 + (i-1) * margin

       xright <- j*m_width - (m_width - dim_x)/2 + (j-1) * margin

       ytop <- (i-1)*m_height + (m_height - dim_y)/2 + (i-1) * margin

-      if(plottingParam$display = "all"){

+

+      # If Images should be saved

+      if(!is.null(plottingParam$save_image) && plottingParam$display == "single"){

+        image_location <- plottingParam$save_image$filename

+        image_scale <- plottingParam$save_image$scale

+        cur_ext <- file_ext(image_location)

+

+        # File name

+        cur_name <- paste0(file_path_sans_ext(image_location),

+                           "_", ind, ".", cur_ext)

+        if(cur_ext == "png"){

+          png(cur_name, width = image_scale * dim_x,

+              height = image_scale * dim_y, units = "px",

+              pointsize = 12 * image_scale)

+        } else if(cur_ext == "jpeg"){

+          jpeg(image_location, width = image_scale * dim_x,

+               height = image_scale * dim_y, units = "px",

+               pointsize = 12 * image_scale)

+        } else if(cur_ext == "tiff"){

+          tiff(image_location, width = image_scale * dim_x,

+               height = image_scale * dim_y, units = "px",

+               pointsize = 12 * image_scale)

+        }

+

+        cur_par <- par(bty="n", mai=c(0,0,0,0), xaxs="i",

+                       yaxs="i", xaxt="n", yaxt="n", col = "white")

+        on.exit(par(cur_par))

+      }

+

+      if(plottingParam$display == "all"){

         rasterImage(Image(out_img[[ind]]),

                     xleft,

                     ybottom,

                     xright,

                     ytop)

       } else {

+        plot(c(0, dim_x), c(0, dim_y), type="n", xlab="", ylab="",

+             asp = 1, ylim = rev(c(0, dim_y)))

         rasterImage(Image(out_img[[ind]]),

                     xleft = 0,

                     ybottom = dim_y,

@@ -411,29 +443,53 @@

       if(ind != legend_ind && !is.null(plottingParam$scale_bar)){

         if(plottingParam$scale_bar$frame == "all"){

-          # Plot scale bar

-          .plotScaleBar(plottingParam$scale_bar,

-                        xleft = 0, xright = dim_x,

-                        ytop = 0, ybottom = dim_y,

-                        image_scale)

+          if(plottingParam$display == "all"){

+            .plotScaleBar(plottingParam$scale_bar,

+                          xl = xleft, xr = xright,

+                          yt = ytop, yb = ybottom,

+                          image_scale)

+          } else {

+            .plotScaleBar(plottingParam$scale_bar,

+                          xl = 0, xr = dim_x,

+                          yt = 0, yb = dim_y,

+                          image_scale)

+          }

         } else {

           cur_ind <- legend_ind + as.integer(plottingParam$scale_bar$frame)

           if(ind == cur_ind && !is.null(plottingParam$scale_bar)){

-            # Plot scale bar

-            .plotScaleBar(plottingParam$scale_bar,

-                          xleft = 0, xright = dim_x,

-                          ytop = 0, ybottom = dim_y,

-                          image_scale)

+            if(plottingParam$display == "all"){

+              .plotScaleBar(plottingParam$scale_bar,

+                            xl = xleft, xr = xright,

+                            yt = ytop, yb = ybottom,

+                            image_scale)

+              } else {

+                .plotScaleBar(plottingParam$scale_bar,

+                            xl = 0, xr = dim_x,

+                            yt = 0, yb = dim_y,

+                            image_scale)

+              }

             }

           }

         }

       # Plot title on images

       if(ind != legend_ind && !is.null(plottingParam$image_title)){

-        .plotImageTitle(out_img, mask, image, img_id,

-                        ind, legend_ind, plottingParam$image_title, dim_x,

-                        xleft = 0, xright = dim_x,

-                        ytop = 0, ybottom = dim_y)

+        if(plottingParam$display == "all"){

+          .plotImageTitle(out_img, mask, image, img_id,

+                          ind, legend_ind, plottingParam$image_title, dim_x,

+                          xl = xleft, xr = xright,

+                          yt = ytop, yb = ybottom)

+        } else {

+          .plotImageTitle(out_img, mask, image, img_id,

+                          ind, legend_ind, plottingParam$image_title, dim_x,

+                          xl = 0, xr = dim_x,

+                          yt = 0, yb = dim_y)

+        }

+      }

+

+      # Close device

+      if(!is.null(plottingParam$save_image) && plottingParam$display == "single"){

+        dev.off()

       }

       if(plottingParam$return_plot && plottingParam$display == "single"){

@@ -493,11 +549,14 @@

   if(!is.null(colour_by) &&

      (all(colour_by %in% rownames(object)) || !is.null(image))){

+    # Maximum title width

+    title_width <- max(strwidth(colour_by, font = colour_by.title.font))

+

     # Maximum label width

     if(is.null(image)){

       all_max <- max(assay(object, exprs_values)[colour_by,])

     } else {

-      all_max <- max(getChannels(image, colour_by)[[1]])

+      all_max <- unlist(lapply(getChannels(image, colour_by), max))

     }

     label_width <- max(strwidth(format(round(all_max, 1), nsmall = 1)))

@@ -524,6 +583,13 @@

                         format(round(cur_max/2, 1), nsmall = 1),

                         format(round(cur_max, 1), nsmall = 1))

+        # Define title cex

+        if(is.null(colour_by.title.cex)){

+          title_cex <- (cur_space_x/1.5)/title_width

+        } else {

+          title_cex <- colour_by.title.cex

+        }

+

         # Define label cex

         if(is.null(colour_by.labels.cex)){

           label_cex <- (cur_space_x/2)/label_width

@@ -536,7 +602,7 @@

         text(x = cur_x, y = cur_y - cur_space_y/2,

              label = colour_by[i], col = "black",

              font = colour_by.title.font,

-             cex = colour_by.title.cex, adj = c(0.5, 1))

+             cex = title_cex, adj = c(0.5, 1))

         text(x=cur_x- cur_space_x/4 + 2,

              y = seq(cur_y - cur_space_y/2 + cur_space_y/4,

                      cur_y + cur_space_y/2 - cur_space_y/8, length.out = 3),

@@ -566,13 +632,22 @@

                       format(round(cur_max/2, 1), nsmall = 1),

                       format(round(cur_max, 1), nsmall = 1))

       label_width <- max(strwidth(rev(cur_labels)))

+      title_width <- strwidth(colour_by, font = colour_by.title.font)

       cur_legend <- as.raster(matrix(rev(colorRampPalette(cur_col$colour_by[[1]])(101)),

                                      ncol=1))

+

+      # Define title cex

+      if(is.null(colour_by.title.cex)){

+        title_cex <- (cur_space_x/1.5)/title_width

+      } else {

+        title_cex <- colour_by.title.cex

+      }

+

       text(x = cur_x + cur_space_x/2, y = cur_y,

            label = colour_by, col = "black",

            font = colour_by.title.font,

-           cex = colour_by.title.cex, adj = c(0.5, 1))

+           cex = title_cex, adj = c(0.5, 1))

       # Define label cex

       if(is.null(colour_by.labels.cex)){

@@ -634,13 +709,22 @@

                       format(round(cur_max/2, 1), nsmall = 1),

                       format(round(cur_max, 1), nsmall = 1))

       label_width <- max(strwidth(rev(cur_labels)))

+      title_width <- strwidth(outline_by, font = colour_by.title.font)

       cur_legend <- as.raster(matrix(rev(colorRampPalette(cur_col$outline_by[[1]])(101)),

                                      ncol=1))

+

+      # Define title cex

+      if(is.null(colour_by.title.cex)){

+        title_cex <- (cur_space_x/1.5)/title_width

+      } else {

+        title_cex <- outline_by.title.cex

+      }

+

       text(x = cur_x + cur_space_x/2, y = cur_y,

            label = outline_by, col = "black",

            font = outline_by.title.font,

-           cex = outline_by.title.cex, adj = c(0.5, 1))

+           cex = title_cex, adj = c(0.5, 1))

       # Define label cex

       if(is.null(outline_by.labels.cex)){

@@ -732,7 +816,7 @@

 #' @importFrom graphics strwidth strheight text rasterImage legend

 #' @importFrom raster as.raster

 .plotImageTitle <- function(out_img, mask, image, img_id, ind, legend_ind, image_title, dim_x,

-                            xleft, xright, ytop, ybottom){

+                            xl, xr, yt, yb){

   if(!is.null(image_title$text)){

     cur_title <- image_title$text[ind - legend_ind]

@@ -753,31 +837,32 @@

   cur_margin.y <- image_title$margin[2]

   cur_font <- image_title$font

-  text_params <- list(labels = cur_title, col = cur_col, cex = cur_cex, font = cur_font)

+  text_params <- list(labels = cur_title, col = cur_col,

+                      cex = cur_cex, font = cur_font)

   if(cur_position == "top"){

-    do.call(text, append(list(x = xleft + dim_x/2,

-                              y = ytop + cur_margin.y,

+    do.call(text, append(list(x = xl + dim_x/2,

+                              y = yt + cur_margin.y,

                               adj = 0.5), text_params))

   } else if(cur_position == "bottom"){

-    do.call(text, append(list(x = xleft + dim_x/2,

-                              y = ybottom - cur_margin.y,

+    do.call(text, append(list(x = xl + dim_x/2,

+                              y = yb - cur_margin.y,

                               adj = 0.5), text_params))

   } else if(cur_position == "topleft"){

-    do.call(text, append(list(x = xleft + cur_margin.x,

-                              y = ytop + cur_margin.y,

+    do.call(text, append(list(x = xl + cur_margin.x,

+                              y = yt + cur_margin.y,

                               adj = 0), text_params))

   } else if(cur_position == "topright"){

-    do.call(text, append(list(x = xright - cur_margin.x,

-                              y = ytop + cur_margin.y,

+    do.call(text, append(list(x = xr - cur_margin.x,

+                              y = yt + cur_margin.y,

                               adj = 1), text_params))

   } else if(cur_position == "bottomleft"){

-    do.call(text, append(list(x = xleft + cur_margin.x,

-                              y = ybottom - cur_margin.y,

+    do.call(text, append(list(x = xl + cur_margin.x,

+                              y = yb - cur_margin.y,

                               adj = 0), text_params))

   } else if(cur_position == "bottomright"){

-    do.call(text, append(list(x = xright - cur_margin.x,

-                              y = ybottom - cur_margin.y,

+    do.call(text, append(list(x = xr - cur_margin.x,

+                              y = yb - cur_margin.y,

                               adj = 1), text_params))

   }

 }

@@ -8,6 +8,9 @@

 \alias{normalize}

 \alias{normalize,ImageList-method}

 \title{Manipulating ImageList objects}

+\value{

+An ImageList object containing the manipulated Images

+}

 \description{

 Methods to change pixel values in ImageList objects. In the

   following sections, \code{object} is an \linkS4class{ImageList} object

@@ -63,7 +66,7 @@ clipping range of the input intensity values (see

 \examples{

 data(pancreasImages)

-# Scale images to create segmentaion masks

+# Scale images to create segmentation masks

 cur_files <- list.files(system.file("extdata", package = "SingleCellMapper"),

                         pattern = "mask.tiff", full.names = TRUE)

 x <- loadImages(cur_files)

@@ -13,6 +13,16 @@

 \item{image_title}{TODO}

 \item{save_image}{TODO}

+

+\item{return_plot}{TODO}

+

+\item{return_images}{TODO}

+

+\item{legend}{TODO}

+

+\item{margin}{TODO}

+

+\item{display}{TODO}

 }

 \value{

 TODO

@@ -23,10 +33,7 @@ TODO

 \section{Setting further parameters}{

 TODO

-# legend list(title, size) also allow NULL

-# return_plot TODO

-# return_images TODO

-# margin between images

+# scale TRUE FALSE

 }

 \examples{

@@ -527,11 +527,56 @@ test_that("plotting-param: images can be plotted individually.", {

   data("pancreasMasks")

   data("pancreasSCE")

+  #' @param missing_colour TODO

+  #' @param background_colour TODO

+  #' @param scale_bar TODO

+  #' @param image_title TODO

+  #' @param save_image TODO

+  #' @param return_plot TODO

+  #' @param return_images TODO

+  #' @param legend TODO

+  #' @param margin TODO

+  #' @param display TODO

+

   # Works

+  expect_silent(plotPixels(pancreasImages, colour_by = c("H3", "SMA")))

+  expect_silent(plotPixels(pancreasImages, display = "all"))

+  expect_silent(plotPixels(pancreasImages, display = "single"))

+  expect_silent(plotPixels(pancreasImages, colour_by = c("H3", "SMA", "CD44"),

+                           display = "single"))

+  expect_silent(plotPixels(pancreasImages, colour_by = c("H3", "SMA", "CD44"),

+                           scale_bar = list(frame = 3),

+                           display = "single"))

+  # scale_bar

+  expect_silent(plotPixels(pancreasImages, colour_by = c("H3", "SMA", "CD44"),

+                           scale_bar = list(position = "topright",

+                                            frame = 3,

+                                            margin = c(20,20)),

+                           display = "single"))

+

+  # image_title

+  expect_silent(plotPixels(pancreasImages, colour_by = c("H3", "SMA", "CD44"),

+                           image_title = list(text = c(1,2,3),

+                                              cex = 3),

+                           display = "single"))

+

+  # image_title

+  expect_silent(plotPixels(pancreasImages, colour_by = c("H3", "SMA", "CD44"),

+                           image_title = list(text = c(1,2,3),

+                                              cex = 3),

+                           display = "single"))

+

+  # save_image

+  expect_silent(plotPixels(pancreasImages, colour_by = c("H3", "SMA", "CD44"),

+                           save_image = list(filename = "~/Desktop/test.png",

+                                             scale = 10),

+                           display = "single"))

+

+  # Fix height of image title and legend

+

+

+  # Check with all other entries

-  # Check return plot

-  # check scale bar and names

-  # check save_image

   expect_silent(plotPixels(pancreasImages))

   expect_silent(plotPixels(pancreasImages, margin = 2))