R 用矩形而不是文本绘制图 [英] R Draws Plots with Rectangles Instead of Text

问题描述

我正在使用 snakemake 构建管道，并使用 conda 和 singularity 环境来确保可重复性.我遇到了一个错误，我的绘图上的文本被矩形替换了

I'm building a pipeline with snakemake and using conda and singularity environments to ensure reproducibility. I run into an error where the text on my plots is replaced by rectangles

在Linux和Mac系统上对管道进行了实验并禁用了奇点容器之后，问题似乎是由于缺少字体库而引起的，因为当我仅使用 conda (-use-conda )在我的Mac上.

After experimenting with the pipeline on Linux and Mac systems and disabling the singularity container, it appears the issue stems from a missing font library as the text is drawn normally when I only run the pipeline using only conda (--use-conda) on my Mac.

奇异容器由使用Debian GNU/Linux.我设法创建了一个最小的示例管道，该管道不会绘制文本.

The singularity container is built from this miniconda docker image that uses Debian GNU/Linux. I've managed to create a minimal example pipeline where the text doesn't get drawn.

# Snakefile
singularity: "docker://continuumio/miniconda3"

rule all:
    input:
        "mtcars-plot.png"

rule plot_mtcars:
    output:
        "mtcars-plot.png"
    conda:
        "minimal.yaml"
    script:
        "mtcars-test.R"

# mtcars-test.R
library(ggplot2)
png("mtcars-plot.png")
ggplot(mtcars, aes(factor(cyl), mpg)) + geom_boxplot()
dev.off()

# minimal.yaml
channels:
    - bioconda
    - conda-forge
    - defaults
dependencies:
    - r-base =3.6
    - r-ggplot2

要绘制折线图，​​请运行管道

To draw the broken plot, run the pipeline

snakemake --use-conda --use-singularity

在Debian GNU/Linux上使用R正确绘制文本时，我可能缺少哪些软件包/库?

What packages/libraries could I be missing to correctly draw text with R on Debian GNU/Linux?

推荐答案

感谢MrFlick的评论，第二个链接说，在R中支持文本需要 mscorefonts 包.

Thanks to MrFlick's comment, the second link says the mscorefonts package is needed for text support in R.

在 conda 环境中添加 mscorefonts 可解决此问题

Adding mscorefonts to the conda environment fixes the issue

# minimal.yaml
channels:
    - bioconda
    - conda-forge
    - defaults
dependencies:
    - r-base =3.6
    - r-ggplot2
    - mscorefonts

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