环境设置函数为options()，用options()命令可以设置一些环境变量，使用help(options)可以查看详细的参数信息。
1. 查看默认参数：
names(options())
[1] "add.smooth" "ambiguousMethodSelection" "askpass"
[4] "asksecret" "BioC" "bitmapType"
[7] "browser" "browserNLdisabled" "buildtools.check"
[10] "buildtools.with" "callr.condition_handler_cli_message" "CBoundsCheck"
[13] "check.bounds" "citation.bibtex.max" "connectionObserver"
[16] "continue" "contrasts" "cpp11_preserve_xptr"
[19] "cpp11_should_unwind_protect" "datatable.alloccol" "datatable.allow.cartesian"
[22] "datatable.auto.index" "datatable.dfdispatchwarn" "datatable.optimize"
[25] "datatable.print.class" "datatable.print.colnames" "datatable.print.keys"
[28] "datatable.print.nrows" "datatable.print.rownames" "datatable.print.topn"
[31] "datatable.print.trunc.cols" "datatable.use.index" "datatable.verbose"
[34] "datatable.warnredundantby" "defaultPackages" "demo.ask"
[37] "deparse.cutoff" "deparse.max.lines" "device"
[40] "device.ask.default" "digits" "download.file.method"
[43] "dplyr.show_progress" "dvipscmd" "echo"
[46] "editor" "encoding" "error"
[49] "example.ask" "expressions" "foreachDoparLocal"
[52] "ggvis.renderer" "help_type" "help.search.types"
[55] "help.try.all.packages" "HTTPUserAgent" "httr_oauth_cache"
[58] "httr_oob_default" "install.packages.compile.from.source" "internet.info"
[61] "keep.parse.data" "keep.parse.data.pkgs" "keep.source"
[64] "keep.source.pkgs" "locatorBell" "mailer"
[67] "matprod" "matrixStats.center.onScalar" "matrixStats.vars.formula.freq"
[70] "matrixStats.vars.formula.onMistake" "max.print" "menu.graphics"
[73] "mgcv.vc.logrange" "na.action" "nwarnings"
[76] "OutDec" "page_viewer" "pager"
[79] "papersize" "pboptions" "PCRE_limit_recursion"
[82] "PCRE_study" "PCRE_use_JIT" "pdfviewer"
[85] "pkgType" "plumber.docs.callback" "plumber.swagger.url"
[88] "printcmd" "profvis.keep_output" "profvis.print"
[91] "profvis.prof_extension" "profvis.prof_output" "progressr.clear"
[94] "progressr.enable" "progressr.enable_after" "progressr.interrupt.message"
[97] "progressr.interrupts" "progressr.interval" "progressr.lifecycle.progress"
[100] "progressr.times" "prompt" "readr.show_progress"
[103] "repos" "restart" "reticulate.initialized"
[106] "reticulate.repl.busy" "reticulate.repl.hook" "reticulate.repl.initialize"
[109] "reticulate.repl.teardown" "rl_word_breaks" "rsconnect.check.certificate"
[112] "rstudio.notebook.executing" "RStudioGD.antialias" "RStudioGD.backend"
[115] "scipen" "Seurat.checkdots" "Seurat.coords.short_range"
[118] "Seurat.input.sparse_ratio" "Seurat.limma.wilcox.msg" "Seurat.memsafe"
[121] "Seurat.Rfast2.msg" "Seurat.warn.umap.uwot" "Seurat.warn.vlnplot.split"
[124] "shiny.launch.browser" "shinygadgets.showdialog" "show.coef.Pvalues"
[127] "show.error.messages" "show.signif.stars" "str"
[130] "str.dendrogram.last" "stringsAsFactors" "terminal.manager"
[133] "texi2dvi" "timeout" "ts.eps"
[136] "ts.S.compat" "unzip" "useFancyQuotes"
[139] "verbose" "viewer" "warn"
[142] "warning.length" "width"
查看默认参数的默认设置getOption()
getOption("stringsAsFactors")
[1] FALSE
getOption("Seurat.checkdots")
[1] "warn"
查看所有默认参数的设置
sapply(names(options()),getOption)
默认参数的更改
options(stringsAsFactors = "TRUE")
getOption("stringsAsFactors")
[1] "TRUE"
2. 一些常见的options设置
- 拼图
options(repr.plot.height=10, repr.plot.width=10)
VlnPlot(pbmc,features = c("nCount_RNA","nFeature_RNA","percent.mito"),pt.size = 0,ncol=1)
拼图之前，先要根据自己图片的张数，设置好画布大小，这很重要。一般一张方形的图会设置为width和height都等于5，如果两张横着拼在一起，就会设画布为10*5；如果拼6张图，一行三张，则设为15*10，以此类推。当然画图的时候也可以自己尝试，根据实际情况调整。
repr.plot.height和repr.plot.width设置了整张图的大小
参考：https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/options
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