Merge pull request #139 from omnideconv/maria2

changed the if order-colorpalettes
omnideconv · Mar 25, 2024 · c9bd2ef · c9bd2ef
2 parents 3ce65bb + 1aee0c5
commit c9bd2ef
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Showing 6 changed files with 30 additions and 10 deletions.
diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml
@@ -41,8 +41,11 @@ jobs:
       - name: Install pak
         run: Rscript -e "install.packages('pak', repos='https://cran.rstudio.com/')"
 
+      - name: Install Devtools
+        run: Rscript -e "pak::pkg_install('devtools')"
+
       - name: Install SpatialExperiment
-        run: Rscript -e "pak::pkg_install('drighelli/SpatialExperiment')"
+        run: Rscript -e "devtools::install_github('drighelli/SpatialExperiment')"
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

diff --git a/.github/workflows/roxygenize.yml b/.github/workflows/roxygenize.yml
@@ -33,8 +33,14 @@ jobs:
       - name: Install pak
         run: Rscript -e "install.packages('pak', repos='https://cran.rstudio.com/')"
 
+      #- name: Install SpatialExperiment
+      # run: Rscript -e "pak::pkg_install('drighelli/SpatialExperiment')"
+
+      - name: Install Devtools
+        run: Rscript -e "pak::pkg_install('devtools')"
+
       - name: Install SpatialExperiment
-        run: Rscript -e "pak::pkg_install('drighelli/SpatialExperiment')"
+        run: Rscript -e "devtools::install_github('drighelli/SpatialExperiment')"
 
       - name: Install dependencies
         uses: r-lib/actions/setup-r-dependencies@v2

diff --git a/.github/workflows/test-coverage.yml b/.github/workflows/test-coverage.yml
@@ -37,8 +37,14 @@ jobs:
       - name: Install pak
         run: Rscript -e "install.packages('pak', repos='https://cran.rstudio.com/')"
 
+      # - name: Install SpatialExperiment
+      # run: Rscript -e "pak::pkg_install('drighelli/SpatialExperiment')"
+
+      - name: Install Devtools
+        run: Rscript -e "pak::pkg_install('devtools')"
+
       - name: Install SpatialExperiment
-        run: Rscript -e "pak::pkg_install('drighelli/SpatialExperiment')"
+        run: Rscript -e "devtools::install_github('drighelli/SpatialExperiment')"
 
       - name: Install Immunedeconv
         run: Rscript -e "pak::pkg_install('omnideconv/immunedeconv')"

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -67,8 +67,14 @@ jobs:
       #- name: Giotto
       #  run: Rscript -e "pak::pkg_install('drieslab/Giotto@master')"
 
+      - name: Install Devtools
+        run: Rscript -e "pak::pkg_install('devtools')"
+
+      - name: Install SpatialExperiment
+        run: Rscript -e "devtools::install_github('drighelli/SpatialExperiment')"
+
       - name: Install Test Dependencies
-        run: Rscript -e "pak::pkg_install(c('drighelli/SpatialExperiment', 'testthat', 'omnideconv/immunedeconv', 'omnideconv/omnideconv', 'satijalab/seurat'))"
+        run: Rscript -e "pak::pkg_install(c('testthat', 'omnideconv/immunedeconv', 'omnideconv/omnideconv', 'satijalab/seurat'))" # drighelli/SpatialExperiment'
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: spacedeconv
 Title: Unified Interface to spatial transcriptomics deconvolution tools
-Version: 0.1.0
+Version: 0.1.1
 Authors@R: 
     person(given="Constantin", family="Zackl", email="constantin.zackl@student.uibk.ac.at", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1991-6943"))
 Description: Collection of 31 deconvolution tools for spatial transcriptomics data.

diff --git a/R/visualization.R b/R/visualization.R
@@ -300,7 +300,10 @@ plot_most_abundant <- function(spe, method = NULL, cell_type = NULL, remove = NU
   num_colors_needed <- length(all_cell_types) - 1 # Number of celltypes
 
   # Determine the palette type and generate colors
-  if (is.character(palette) && palette %in% rownames(RColorBrewer::brewer.pal.info)) {
+  if (is.vector(palette) && length(palette) > 1 && all(sapply(palette, is.character))) { # the manual comes first
+    # Custom color vector
+    color_vector <- palette
+  } else if (is.character(palette) && palette %in% rownames(RColorBrewer::brewer.pal.info)) {
     # RColorBrewer palette
     brewer_palette <- RColorBrewer::brewer.pal(RColorBrewer::brewer.pal.info[palette, "maxcolors"], palette)
     color_vector <- colorRampPalette(brewer_palette)(num_colors_needed)
@@ -315,9 +318,6 @@ plot_most_abundant <- function(spe, method = NULL, cell_type = NULL, remove = NU
     } else {
       stop("Invalid palette type.")
     }
-  } else if (is.vector(palette) && all(sapply(palette, is.character))) {
-    # Custom color vector
-    color_vector <- palette
   } else {
     stop("Invalid palette input.")
   }
@@ -326,7 +326,6 @@ plot_most_abundant <- function(spe, method = NULL, cell_type = NULL, remove = NU
   custom_colors <- c(color_vector, "#D3D3D3")
   names(custom_colors) <- all_cell_types
 
-
   return(make_baseplot(
     spe = spe, df = df2, to_plot = "mostAbundant", palette = custom_colors,
     sample_id = sample_id, image_id = image_id, background = background, zoom = zoom,