Merge pull request #22 from BodenmillerGroup/fullscreen

Change default display area and default colors
BodenmillerGroup · Oct 19, 2023 · a116e36 · a116e36
2 parents 20e166c + b5de6e2
commit a116e36
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: cytoviewer
-Version: 1.1.2
+Version: 1.1.3
 Title: An interactive multi-channel image viewer for R
 Description: 
     This R package supports interactive visualization of multi-channel images 

diff --git a/NEWS b/NEWS
@@ -1,30 +1,23 @@
 Changes in version 0.1.0 (2022-11-14):
-
 + initial version
 
 Changes in version 0.1.1 (2022-11-18):
-
 + first working version
 
 Changes in version 0.1.2 (2022-11-28):
-
 + allow selecting of cell types
 
 Changes in version 0.1.5 (2023-02-14):
-
 + small fixes to solve check issues
 
 Changes in version 0.1.6 (2023-02-23):
-
 + public release of cytoviewer on GitHub
 + main functionality done
 
 Changes in version 0.99.0 (2023-03-23):
-
 + code preparations for Bioconductor submission
 
 Changes in version 0.99.1 (2023-04-12):
-
 + code adjustments after Bioconductor approval
 + included reactive image / mask reading
 
@@ -42,4 +35,7 @@ Changes in version 1.0.1 (2023-07-27):
 + added more tests and validation checks
 
 Changes in version 1.1.2 (2023-10-09): 
-+ vignette updates
++ vignette updates
+
+Changes in version 1.1.3 (2023-10-19): 
++ enlarged default display area and changed default color settings
diff --git a/R/interface_cytoviewer.R b/R/interface_cytoviewer.R
@@ -203,7 +203,6 @@
                              colourInput(inputId = "color6", label = "Color", 
                                          value = "blue")),
                     hr(),
-                    #icon = icon("fas fa-sliders-h"), 
                     startExpanded = FALSE),
             menuItem("Advanced controls",
                      checkboxInput("outline", "Show cell outlines", 
@@ -266,7 +265,7 @@
                  tabsetPanel(
                    tabPanel("Composite",box(
                      withSpinner(
-                       svgPanZoomOutput("imagePlot"), type = 6), 
+                         svgPanZoomOutput("imagePlot", width = "100%", height = "75vh"), type = 6), 
                      title = NULL, id = "expression", status = "primary", 
                      width = 12, height = NULL)),
                    tabPanel("Channels", value = "tiles_tab", width = 12, 

diff --git a/R/utils_cytoviewer.R b/R/utils_cytoviewer.R
@@ -336,7 +336,7 @@
     if (input$outline && !is.null(input$outline_by)){
       if (input$outline_by == "") {
 
-        req(img_id)
+        req(img_id, cur_markers)
 
         cur_mask <- .get_mask(input, mask, img_id, cur_image)
 
@@ -356,7 +356,7 @@
 
         } else if (input$outline_by != "") { 
 
-        req(img_id, cell_id) 
+        req(img_id, cell_id, cur_markers) 
 
         validate(
           need(is.null(dim(colData(object)[[input$outline_by]])), 
@@ -486,7 +486,7 @@
     if (input$outline && !is.null(input$outline_by)){
       if(input$outline_by == "") {
 
-        req(img_id)
+        req(img_id, markers)
 
         cur_mask <- .get_mask(input, mask, img_id, cur_image)
 
@@ -507,7 +507,7 @@
 
     } else if (input$outline_by != "") {
 
-      req(img_id, cell_id) 
+      req(img_id, cell_id, markers) 
 
       cur_entries <- length(unique(colData(object)[[input$outline_by]]))
 
@@ -742,8 +742,8 @@
                       style = "color: black;padding-top: 0px"), 
                  style = "color: black; padding-top: 0px",
                  lapply(seq_along(input$select_outline), function (i){
-                   cur_col <- c(brewer.pal(12, "Paired"),
-                                brewer.pal(8, "Pastel2")[-c(3,5,8)],
+                   cur_col <- c(brewer.pal(9, "Set1"),
+                                brewer.pal(8, "Pastel2"),
                                 brewer.pal(12, "Set3")[-c(2,3,8,9,11,12)])
                    colourInput(inputId = paste0("color_outline",i),
                                label = if (is.logical(colData(object)[[input$outline_by]])) {
@@ -882,8 +882,8 @@
                         style = "color: black;padding-top: 0px"), 
                    style = "color: black; padding-top: 0px",
                    lapply(seq_along(input$color_by_selection), function (i){
-                     cur_col <- c(brewer.pal(12, "Paired"),
-                                  brewer.pal(8, "Pastel2")[-c(3,5,8)],
+                     cur_col <- c(brewer.pal(9, "Set1"),
+                                  brewer.pal(8, "Pastel2"),
                                   brewer.pal(12, "Set3")[-c(2,3,8,9,11,12)])
                      colourInput(inputId = paste0("color_by",i),
                                  label = if (is.logical(colData(object)[[input$color_by]])) {
@@ -1072,7 +1072,7 @@
                            image, img_id, cell_id){
   renderUI({
     if(input$plotcells){
-    box(withSpinner(svgPanZoomOutput("cellsPlot"),type = 6), 
+    box(withSpinner(svgPanZoomOutput("cellsPlot", width = "100%",height = "75vh"),type = 6), 
           title = NULL, 
           id = "expression",
           status = "primary",

diff --git a/README.md b/README.md
@@ -4,8 +4,9 @@
 
 <!-- badges: start -->
 
-[![codecov](https://codecov.io/gh/BodenmillerGroup/cytoviewer/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/BodenmillerGroup/cytoviewer/tree/devel)
 [![docs](https://github.com/BodenmillerGroup/cytoviewer/actions/workflows/docs.yml/badge.svg)](https://github.com/BodenmillerGroup/cytoviewer/actions/workflows/docs.yml)
+[![codecov](https://codecov.io/gh/BodenmillerGroup/cytoviewer/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/BodenmillerGroup/cytoviewer/tree/devel)
+
 
 <!-- badges: end -->
 
@@ -17,16 +18,17 @@ cytometry and other highly multiplexed imaging techniques. The
 `cytoviewer` package is divided into image-level (Composite and
 Channels) and cell-level visualization (Masks). It allows users 
 to overlay individual images with segmentation masks, integrates well 
-with [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html)
-and [SpatialExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html)
-objects for metadata visualization and supports image downloads.
+with [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) / [SpatialExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) 
+and [CytoImageList](https://www.bioconductor.org/packages/release/bioc/html/cytomapper.html)
+objects for metadata and image visualization and supports image downloads.
 
 ## Check status
 
 | Bioc branch |                                                                                                     Checks                                                                                                      |
 |:------------------------------------------:|:--------------------------:|
-|   Release   | [![build-check-release](https://github.com/BodenmillerGroup/cytoviewer/workflows/build-checks-release/badge.svg)](https://github.com/BodenmillerGroup/cytoviewer/actions?query=workflow%3Abuild-checks-release) |
-|    Devel    |    [![build-check-devel](https://github.com/BodenmillerGroup/cytoviewer/workflows/build-checks-devel/badge.svg)](https://github.com/BodenmillerGroup/cytoviewer/actions?query=workflow%3Abuild-checks-devel)    |
+|   Release   | [![build-checks-release](https://github.com/BodenmillerGroup/cytoviewer/actions/workflows/build-checks-release.yml/badge.svg?branch=devel)](https://github.com/BodenmillerGroup/cytoviewer/actions/workflows/build-checks-release.yml) |
+|    Devel    | [![build-checks-devel](https://github.com/BodenmillerGroup/cytoviewer/actions/workflows/build-checks-devel.yml/badge.svg?branch=devel)](https://github.com/BodenmillerGroup/cytoviewer/actions/workflows/build-checks-devel.yml) |
+
 
 ## Requirements
 
@@ -62,7 +64,7 @@ To load the package in your R session, type the following:
 library(cytoviewer)
 ```
 
-## Usage
+## Basic usage
 
 ``` r
 library(cytoviewer)
@@ -82,11 +84,14 @@ app <- cytoviewer(image = pancreasImages,
 
 if (interactive()) {
 
-  shiny::runApp(app, launch.browser = TRUE)
+  shiny::runApp(app)
 
   }
 ```
 
+For more detailed information on package usage and functionality, 
+please refer to [https://bodenmillergroup.github.io/cytoviewer/](https://bodenmillergroup.github.io/cytoviewer/). 
+
 ## Contributing
 
 For feature requests, please open an issue