Merge pull request #63 from morinlab/kdreval-viz-setup

bug fix: handling of custom colors for numeric annotations
morinlab · Jul 15, 2024 · f12f964 · f12f964
2 parents cabfacf + 4e2d594
commit f12f964
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diff --git a/.github/workflows/build_check.yaml b/.github/workflows/build_check.yaml
@@ -35,11 +35,11 @@ jobs:
 
     - name: Build package
       run:
-        Rscript -e "devtools::install(repos = BiocManager::repositories())"
+        Rscript --vanilla -e "devtools::install(repos = BiocManager::repositories(), upgrade = FALSE)"
 
     - name: Check package
       run:
-        Rscript -e "devtools::check(vignettes = FALSE, args = '--no-examples')"
+        Rscript --vanilla -e "devtools::check(vignettes = FALSE, args = '--no-examples')"
 
     - name: Upload check results
       if: failure()

diff --git a/R/prettyOncoplot.R b/R/prettyOncoplot.R
@@ -249,6 +249,24 @@ prettyOncoplot = function(maf_df,
         colnames(tsb.include) = tsbs[!tsbs %in% colnames(mat_origin)]
         rownames(tsb.include) = rownames(mat_origin)
         mat_origin = cbind(mat_origin, tsb.include)
+      }else if(length(include_noncoding) > 0){
+        print(
+            "You requested to include noncoding mutations and remove non-mutated patients ..."
+        )
+        these_have_noncoding <- maf_df %>%
+            filter(
+                Tumor_Sample_Barcode %in% patients,
+                Hugo_Symbol %in% names(include_noncoding),
+                Variant_Classification %in% unlist(unname(include_noncoding))
+            ) %>%
+            distinct(
+                Tumor_Sample_Barcode, Hugo_Symbol, Variant_Classification, Start_Position, End_Position
+            ) %>%
+            pull(Tumor_Sample_Barcode)
+        tsb.include = matrix(data = 0, nrow = nrow(mat_origin), ncol = length(these_have_noncoding[!these_have_noncoding %in% colnames(mat_origin)]))
+        colnames(tsb.include) = these_have_noncoding[!these_have_noncoding %in% colnames(mat_origin)]
+        rownames(tsb.include) = rownames(mat_origin)
+        mat_origin = cbind(mat_origin, tsb.include)
       }
       write.table(mat_origin, file = onco_matrix_path, quote = F, sep = "\t")
     }
@@ -700,8 +718,13 @@ prettyOncoplot = function(maf_df,
     replace(is.na(.), "NA")
   # Only keep the annotation colors for the remaining patients
   for(column in colnames(metadata_df)){
-    remaining <- unique(metadata_df[column]) %>% pull()
-    colours[[column]] <- (colours[column] %>% unname %>% unlist)[remaining]
+    if(missing(numericMetadataColumns)){
+        remaining <- unique(metadata_df[column]) %>% pull()
+        colours[[column]] <- (colours[column] %>% unname %>% unlist)[remaining]
+    }else if(!column %in% numericMetadataColumns){
+        remaining <- unique(metadata_df[column]) %>% pull()
+        colours[[column]] <- (colours[column] %>% unname %>% unlist)[remaining]
+    }
   }
 
   ch = ComplexHeatmap::oncoPrint(mat[intersect(genes, genes_kept),patients_kept],

diff --git a/envs/r.yaml b/envs/r.yaml
@@ -1,189 +1,218 @@
-name: r
+name: deps
 channels:
   - conda-forge
   - defaults
 dependencies:
   - _libgcc_mutex=0.1
   - _openmp_mutex=4.5
   - _r-mutex=1.0.1
-  - _sysroot_linux-64_curr_repodata_hack=3
   - binutils_impl_linux-64=2.40
+  - binutils_linux-64=2.40
   - bwidget=1.9.14
   - bzip2=1.0.8
-  - c-ares=1.27.0
-  - ca-certificates=2024.2.2
-  - cairo=1.18.0
-  - curl=8.5.0
+  - c-ares=1.28.1
+  - ca-certificates=2024.7.4
+  - cairo=1.16.0
+  - cmake=3.30.0
+  - curl=8.8.0
   - expat=2.6.2
   - font-ttf-dejavu-sans-mono=2.37
   - font-ttf-inconsolata=3.000
   - font-ttf-source-code-pro=2.038
   - font-ttf-ubuntu=0.83
   - fontconfig=2.14.2
-  - fonts-anaconda=1
   - fonts-conda-ecosystem=1
   - fonts-conda-forge=1
   - freetype=2.12.1
   - fribidi=1.0.10
   - gcc_impl_linux-64=13.2.0
-  - gettext=0.21.1
+  - gcc_linux-64=13.2.0
+  - gettext=0.22.5
+  - gettext-tools=0.22.5
   - gfortran_impl_linux-64=13.2.0
   - graphite2=1.3.13
+  - gsl=2.7
   - gxx_impl_linux-64=13.2.0
-  - harfbuzz=8.3.0
-  - icu=73.2
-  - kernel-headers_linux-64=4.18.0
+  - harfbuzz=7.3.0
+  - icu=72.1
+  - kernel-headers_linux-64=2.6.32
   - keyutils=1.6.1
-  - krb5=1.21.2
+  - krb5=1.21.3
   - ld_impl_linux-64=2.40
   - lerc=4.0.0
+  - libasprintf=0.22.5
+  - libasprintf-devel=0.22.5
   - libblas=3.9.0
-  - libcurl=8.5.0
-  - libdeflate=1.19
+  - libcblas=3.9.0
+  - libcurl=8.8.0
+  - libdeflate=1.18
   - libedit=3.1.20191231
   - libev=4.33
   - libexpat=2.6.2
   - libffi=3.4.2
   - libgcc-devel_linux-64=13.2.0
-  - libgcc-ng=13.2.0
-  - libgfortran-ng=13.2.0
-  - libgfortran5=13.2.0
-  - libgit2=1.7.2
-  - libglib=2.80.0
-  - libgomp=13.2.0
+  - libgcc-ng=14.1.0
+  - libgettextpo=0.22.5
+  - libgettextpo-devel=0.22.5
+  - libgfortran-ng=14.1.0
+  - libgfortran5=14.1.0
+  - libgit2=1.5.1
+  - libglib=2.78.1
+  - libgomp=14.1.0
   - libiconv=1.17
-  - libjpeg-turbo=3.0.0
+  - libjpeg-turbo=2.1.5.1
   - liblapack=3.9.0
   - libnghttp2=1.58.0
-  - libopenblas=0.3.26
+  - libnsl=2.0.1
+  - libopenblas=0.3.27
   - libpng=1.6.43
   - libsanitizer=13.2.0
+  - libsqlite=3.46.0
   - libssh2=1.11.0
   - libstdcxx-devel_linux-64=13.2.0
-  - libstdcxx-ng=13.2.0
-  - libtiff=4.6.0
+  - libstdcxx-ng=14.1.0
+  - libtiff=4.5.1
   - libuuid=2.38.1
-  - libwebp-base=1.3.2
+  - libuv=1.48.0
+  - libwebp-base=1.4.0
   - libxcb=1.15
-  - libxml2=2.12.5
-  - libzlib=1.2.13
-  - lz4-c=1.9.4
+  - libxcrypt=4.4.36
+  - libxml2=2.11.5
+  - libzlib=1.3.1
   - make=4.3
-  - ncurses=6.4
-  - openssl=3.2.1
-  - pandoc=3.1.12.2
-  - pango=1.52.1
-  - pcre2=10.43
+  - mysql-common=8.3.0
+  - mysql-connector-c=6.1.11
+  - mysql-libs=8.3.0
+  - mysqlclient=2.2.4
+  - ncurses=6.5
+  - openssl=3.3.1
+  - pandoc=2.19.2
+  - pango=1.50.14
+  - pcre2=10.40
+  - pip=24.0
   - pixman=0.43.2
   - pthread-stubs=0.4
-  - r-askpass=1.2.0
+  - r-askpass=1.1
   - r-assertthat=0.2.1
-  - r-base=4.2.3
+  - r-backports=1.4.1
+  - r-base=4.1.3
   - r-base64enc=0.1_3
-  - r-biocmanager=1.30.22
-  - r-brew=1.0_10
-  - r-brio=1.1.4
-  - r-bslib=0.6.1
+  - r-biocmanager=1.30.21
+  - r-brew=1.0_8
+  - r-brio=1.1.3
+  - r-bslib=0.5.0
   - r-cachem=1.0.8
-  - r-callr=3.7.5
-  - r-cli=3.6.2
+  - r-callr=3.7.3
+  - r-cli=3.6.1
   - r-clipr=0.8.0
-  - r-commonmark=1.9.1
+  - r-commonmark=1.9.0
   - r-cpp11=0.4.7
   - r-crayon=1.5.2
-  - r-credentials=2.0.1
-  - r-curl=5.1.0
-  - r-desc=1.4.3
+  - r-credentials=1.3.2
+  - r-curl=4.3.3
+  - r-dbi=1.1.3
+  - r-desc=1.4.2
   - r-devtools=2.4.5
   - r-diffobj=0.3.5
-  - r-digest=0.6.35
-  - r-downlit=0.4.3
+  - r-digest=0.6.31
+  - r-downlit=0.4.2
   - r-ellipsis=0.3.2
-  - r-evaluate=0.23
-  - r-fansi=1.0.6
+  - r-evaluate=0.21
+  - r-fansi=1.0.4
   - r-fastmap=1.1.1
-  - r-fontawesome=0.5.2
-  - r-fs=1.6.3
-  - r-gert=2.0.1
+  - r-fontawesome=0.5.1
+  - r-fs=1.6.2
+  - r-gert=1.9.2
   - r-gh=1.4.0
+  - r-git2r=0.31.0
   - r-gitcreds=0.1.2
-  - r-glue=1.7.0
+  - r-glue=1.6.2
   - r-highr=0.10
-  - r-htmltools=0.5.7
-  - r-htmlwidgets=1.6.4
-  - r-httpuv=1.6.14
-  - r-httr=1.4.7
-  - r-httr2=1.0.0
+  - r-htmltools=0.5.5
+  - r-htmlwidgets=1.6.2
+  - r-httpuv=1.6.11
+  - r-httr=1.4.6
+  - r-httr2=0.2.3
   - r-ini=0.3.1
   - r-jquerylib=0.1.4
-  - r-jsonlite=1.8.8
-  - r-knitr=1.45
-  - r-later=1.3.2
-  - r-lifecycle=1.0.4
+  - r-jsonlite=1.8.5
+  - r-knitr=1.43
+  - r-later=1.3.1
+  - r-lattice=0.21_8
+  - r-lifecycle=1.0.3
   - r-magrittr=2.0.3
+  - r-mass=7.3_58.3
+  - r-matrix=1.5_4.1
+  - r-matrixmodels=0.5_0
   - r-memoise=2.0.1
   - r-mime=0.12
   - r-miniui=0.1.1.1
-  - r-openssl=2.1.1
+  - r-openssl=2.0.6
   - r-pillar=1.9.0
-  - r-pkgbuild=1.4.2
+  - r-pbkrtest=0.5.2
+  - r-pkgbuild=1.4.0
   - r-pkgconfig=2.0.3
   - r-pkgdown=2.0.7
-  - r-pkgload=1.3.4
+  - r-pkgload=1.3.2
   - r-praise=1.0.0
-  - r-prettyunits=1.2.0
-  - r-processx=3.8.3
+  - r-prettyunits=1.1.1
+  - r-processx=3.8.1
   - r-profvis=0.3.8
-  - r-promises=1.2.1
-  - r-ps=1.7.6
-  - r-purrr=1.0.2
+  - r-promises=1.2.0.1
+  - r-ps=1.7.5
+  - r-purrr=1.0.1
   - r-r6=2.5.1
-  - r-ragg=1.3.0
+  - r-ragg=1.2.5
   - r-rappdirs=0.3.3
   - r-rcmdcheck=1.4.0
-  - r-rcpp=1.0.12
+  - r-rcpp=1.0.10
   - r-rematch2=2.1.2
-  - r-remotes=2.4.2.1
-  - r-rlang=1.1.3
-  - r-rmarkdown=2.25
-  - r-roxygen2=7.3.1
-  - r-rprojroot=2.0.4
-  - r-rstudioapi=0.15.0
+  - r-remotes=2.4.2
+  - r-rlang=1.1.1
+  - r-rmarkdown=2.22
+  - r-rmysql=0.10.25
+  - r-roxygen2=7.2.3
+  - r-rprojroot=2.0.3
+  - r-rstudioapi=0.14
   - r-rversions=2.1.2
-  - r-sass=0.4.8
+  - r-sass=0.4.6
   - r-sessioninfo=1.2.2
-  - r-shiny=1.8.0
+  - r-shiny=1.7.4
   - r-sourcetools=0.1.7_1
-  - r-stringi=1.8.3
-  - r-stringr=1.5.1
+  - r-stringi=1.7.12
+  - r-stringr=1.5.0
   - r-sys=3.4.2
-  - r-systemfonts=1.0.5
-  - r-testthat=3.2.1
-  - r-textshaping=0.3.7
+  - r-systemfonts=1.0.4
+  - r-testthat=3.1.8
+  - r-textshaping=0.3.6
   - r-tibble=3.2.1
-  - r-tinytex=0.49
+  - r-tinytex=0.45
   - r-urlchecker=1.0.1
-  - r-usethis=2.2.3
-  - r-utf8=1.2.4
-  - r-vctrs=0.6.5
-  - r-waldo=0.5.2
+  - r-usethis=2.2.0
+  - r-utf8=1.2.3
+  - r-vctrs=0.6.2
+  - r-waldo=0.5.1
   - r-whisker=0.4.1
-  - r-withr=3.0.0
-  - r-xfun=0.42
-  - r-xml2=1.3.6
+  - r-withr=2.5.0
+  - r-xfun=0.39
+  - r-xml2=1.3.4
   - r-xopen=1.0.0
   - r-xtable=1.8_4
-  - r-yaml=2.3.8
-  - r-zip=2.3.1
+  - r-yaml=2.3.7
+  - r-zip=2.3.0
   - readline=8.2
+  - rhash=1.4.4
   - sed=4.8
-  - sysroot_linux-64=2.28
+  - setuptools=70.1.1
+  - sysroot_linux-64=2.12
   - tk=8.6.13
   - tktable=2.10
+  - tzdata=2024a
+  - wheel=0.43.0
   - xorg-kbproto=1.0.7
   - xorg-libice=1.1.1
   - xorg-libsm=1.2.4
-  - xorg-libx11=1.8.7
+  - xorg-libx11=1.8.9
   - xorg-libxau=1.0.11
   - xorg-libxdmcp=1.1.3
   - xorg-libxext=1.3.4
@@ -193,5 +222,5 @@ dependencies:
   - xorg-xextproto=7.3.0
   - xorg-xproto=7.0.31
   - xz=5.2.6
-  - zlib=1.2.13
-  - zstd=1.5.5
+  - zlib=1.3.1
+  - zstd=1.5.6