avoid showtext dependency

ggplot falls back to the default font if Noto Sans is unavailable. showtext started causing a cryptic segfault

Author: ahmig

Dockerfile

@@ -1,6 +1,6 @@
 FROM condaforge/miniforge3:latest
 LABEL io.github.snakemake.containerized="true"
-LABEL io.github.snakemake.conda_env_hash="966286962ebc1e35e9809cc85e2904bfefb462e6a14ee09730b81ab69eb4d441"
+LABEL io.github.snakemake.conda_env_hash="fb2a04b98efa75d8b830a16722a8717eb91a3c66659e3c78b90b0cee3a50db69"
 
 # Step 2: Retrieve conda environments
 
@@ -117,12 +117,12 @@ COPY workflow/envs/quarto_render.yaml /conda-envs/96f3c1cec4b3ce5d72f708992272e9
 
 # Conda environment:
 #   source: workflow/envs/renv.yaml
-#   prefix: /conda-envs/8ad6cdcf265d30289788da99d5bf9fff
+#   prefix: /conda-envs/fe892aca096e6b2883923c8755f9ac77
 #   channels:
 #     - conda-forge
 #     - bioconda
 #   dependencies:
-#     - r-base=4.3.2
+#     - r-base=4.3.3
 #     - r-tidyverse==2.0.0
 #     - r-ggrepel==0.9.3
 #     - r-ggpubr==0.6.0
@@ -133,10 +133,9 @@ COPY workflow/envs/quarto_render.yaml /conda-envs/96f3c1cec4b3ce5d72f708992272e9
 #     - r-data.table==1.14.8
 #     - r-future.apply==1.11.0
 #     - r-scales==1.3.0
-#     - r-showtext==0.9_6
 #     - r-logger==0.2.2
-RUN mkdir -p /conda-envs/8ad6cdcf265d30289788da99d5bf9fff
-COPY workflow/envs/renv.yaml /conda-envs/8ad6cdcf265d30289788da99d5bf9fff/environment.yaml
+RUN mkdir -p /conda-envs/fe892aca096e6b2883923c8755f9ac77
+COPY workflow/envs/renv.yaml /conda-envs/fe892aca096e6b2883923c8755f9ac77/environment.yaml
 
 # Conda environment:
 #   source: workflow/envs/snpeff.yaml
@@ -185,7 +184,7 @@ RUN conda env create --prefix /conda-envs/9c24a867826615972cc288081976e7fc --fil
     conda env create --prefix /conda-envs/04a3347f94ddf7e21c34bc49e5246076 --file /conda-envs/04a3347f94ddf7e21c34bc49e5246076/environment.yaml && \
     conda env create --prefix /conda-envs/fb978640cd765c8a63bbcdc01f3a206b --file /conda-envs/fb978640cd765c8a63bbcdc01f3a206b/environment.yaml && \
     conda env create --prefix /conda-envs/96f3c1cec4b3ce5d72f708992272e9c1 --file /conda-envs/96f3c1cec4b3ce5d72f708992272e9c1/environment.yaml && \
-    conda env create --prefix /conda-envs/8ad6cdcf265d30289788da99d5bf9fff --file /conda-envs/8ad6cdcf265d30289788da99d5bf9fff/environment.yaml && \
+    conda env create --prefix /conda-envs/fe892aca096e6b2883923c8755f9ac77 --file /conda-envs/fe892aca096e6b2883923c8755f9ac77/environment.yaml && \
     conda env create --prefix /conda-envs/0adafb79cb1bec58ef4c77bf4cca4f95 --file /conda-envs/0adafb79cb1bec58ef4c77bf4cca4f95/environment.yaml && \
     conda env create --prefix /conda-envs/1f283441022c3c9d97669994a3c5e8bb --file /conda-envs/1f283441022c3c9d97669994a3c5e8bb/environment.yaml && \
     conda env create --prefix /conda-envs/81e46c677a6cc0618c93963d57d17d3f --file /conda-envs/81e46c677a6cc0618c93963d57d17d3f/environment.yaml && \

config/design_plots.R

@@ -1,26 +1,14 @@
-# Jordi Sevilla
-
 library(ggplot2)
-library(showtext)
-
-# Ajustes ####
-showtext_auto(enable = FALSE)
-showtext_opts(dpi = 250)
-
-# Tema
-font_add_google("Noto Sans", "Noto Sans")
-showtext_auto()
 
+# Theme
 theme_set(theme_minimal())
-
 theme_update(
-  text = element_text(size = 16, family = "Noto Sans"),
-  axis.title = element_text(size = 16),
+  text = element_text(size = 10, family = "Noto Sans"),
+  axis.title = element_text(size = 12),
   axis.line = element_line(
     linewidth = 0.5,
     colour = "grey40",
-    linetype = 1,
-    arrow = arrow(length = unit(3, "mm"))
+    linetype = 1
   ),
   panel.grid = element_line(linewidth = 0.17, color = "lightgray")
 )

workflow/envs/renv.yaml

@@ -2,7 +2,7 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - r-base=4.3.2
+  - r-base=4.3.3
   - r-tidyverse==2.0.0
   - r-ggrepel==0.9.3
   - r-ggpubr==0.6.0
@@ -13,5 +13,4 @@ dependencies:
   - r-data.table==1.14.8
   - r-future.apply==1.11.0
   - r-scales==1.3.0
-  - r-showtext==0.9_6
   - r-logger==0.2.2