通过conda安装纯净环境的R绘图合集

发布于 2022-02-24  136 次阅读


  • conda create -n rplot -c conda-forge r-base=4.1.2 -y
  • conda activate rplot
  • conda install -c conda-forge r-seurat=4.1.0 -y
  • conda install -c conda-forge r-irkernel=1.3 -y
  • R
  • IRkernel::installspec(name='rplot', displayname='r-plot')
  • q()

火山图

  • conda install -c bioconda bioconductor-enhancedvolcano=1.12.0 -y

和弦图

  • conda install -c conda-forge r-circlize=0.4.14 -y

热图

  • conda install -c bioconda bioconductor-complexheatmap=2.10.0 -y
  • conda install -c conda-forge r-pheatmap=1.0.12 -y

调色板

  • conda install -c conda-forge r-ggsci=2.9 -y

iRGSEA

  • conda install -c conda-forge r-biocmanager=1.30.16 -y
  • conda install -c conda-forge r-devtools=2.4.3 -y
  • conda install -c conda-forge r-domc=1.3.8 -y
  • R
cran.packages <- c("msigdbr", "dplyr", "purrr", "stringr","magrittr",
                   "RobustRankAggreg", "tibble", "reshape2", "ggsci",
                   "tidyr", "aplot", "ggfun", "ggplotify", "ggridges",
                   "gghalves", "Seurat", "SeuratObject", "methods",
                   "devtools", "BiocManager","data.table","doParallel",
                   "doRNG")
install.packages(cran.packages, ask = F, update = F)
bioconductor.packages <- c("GSEABase", "AUCell", "SummarizedExperiment",
                           "singscore", "GSVA", "ComplexHeatmap", "ggtree",
                           "Nebulosa")
BiocManager::install(bioconductor.packages, ask = F, update = F)
devtools::install_local('~/github_repo/UCell-master.zip')
devtools::install_local('~/github_repo/irGSEA-master.zip')

 

DIY

  • conda install -c conda-forge r-tidyverse=1.3.1 -y
  • conda install -c conda-forge r-ggdendro=0.1.23 -y
  • conda install -c conda-forge r-ggpubr=0.4.0 -y


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