R保存图片

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应用场景

通常我在数据分析的时候，使用Rstudio+Rmarkdown可以实时对数据可视化。一旦一块数据分析的代码成熟后，我会写成pipeline，但是仍然需要导出中间结果的可视化结果，以期对数据进行质控。我对图片质量的要求不高。因此直接采用png格式。

文档太长可以不看。给个例子

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png(filename = "demo.png", width = 8, height = 12, units = "in", res = 300)
# some plots
dev.off()

这里采用inches作为单位，是为了和Rmarkdown统一。此外，如果使用这一单位，必须指定分辨率。一般300dpi即可。

批量绘图

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# On Rstudio
for (module_name in names(module.features)) {
  p.list <- list(
    FeaturePlotMeta(seu.tenX.add_module_score, features = module_name, reduction = "umap", title = paste0(module_name, " (10X)")),
    FeaturePlotMeta(seu.tenX.add_module_score, features = module_name, reduction = "tsne", title = paste0(module_name, " (10X)")),
    FeaturePlotMeta(seu.smart.add_module_score, features = module_name, reduction = "umap", 
                  title = paste0(module_name, " (Smart-seq2)")),
    FeaturePlotMeta(seu.smart.add_module_score, features = module_name, reduction = "tsne", 
                  title = paste0(module_name, " (Smart-seq2)"))
  )
  for (i in 1:length(p.list)) {
    png(filename = paste0("plots/human_gene_module/", module_name, "-", i,".png"), width = 6, height = 5, units = "in", res = 600)
    plot(p.list[[i]]) # 注意这里，一定要用plot，虽然目前我还不知道为什么
    dev.off()
  }
}

相关R文档

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bmp(filename = "Rplot%03d.bmp",
    width = 480, height = 480, units = "px", pointsize = 12,
    bg = "white", res = NA, ...,
    type = c("cairo", "Xlib", "quartz"), antialias)
jpeg(filename = "Rplot%03d.jpeg",
     width = 480, height = 480, units = "px", pointsize = 12,
     quality = 75,
     bg = "white", res = NA, ...,
     type = c("cairo", "Xlib", "quartz"), antialias)
png(filename = "Rplot%03d.png",
    width = 480, height = 480, units = "px", pointsize = 12,
     bg = "white",  res = NA, ...,
    type = c("cairo", "cairo-png", "Xlib", "quartz"), antialias)
tiff(filename = "Rplot%03d.tiff",
     width = 480, height = 480, units = "px", pointsize = 12,
     compression = c("none", "rle", "lzw", "jpeg", "zip", "lzw+p", "zip+p"),
     bg = "white", res = NA,  ...,
     type = c("cairo", "Xlib", "quartz"), antialias)

Arguments

filename the name of the output file. The page number is substituted if a C integer format is included in the character string, as in the default. (The result must be less than PATH_MAX characters long, and may be truncated if not. See postscript for further details.) Tilde expansion is performed where supported by the platform.
width the width of the device.
height the height of the device.
units The units in which height and width are given. Can be px(pixels, the default), in (inches), cm or mm.
pointsize the default pointsize of plotted text, interpreted as big points (1/72 inch) at res ppi.
bg the initial background colour: can be overridden by setting par(“bg”).
quality the ‘quality’ of the JPEG image, as a percentage. Smaller values will give more compression but also more degradation of the image.
compression the type of compression to be used. Ignored for type = "quartz".
res The nominal resolution in ppi which will be recorded in the bitmap file, if a positive integer. Also used for units other than the default, and to convert points to pixels.
... for type = "Xlib" only, additional arguments to the underlying X11 device such as fonts or family.For types "cairo" and "quartz", the family argument can be supplied. See the ‘Cairo fonts’ section in the help for X11.
type character string, one of "Xlib" or "quartz" (some macOS builds) or "cairo". The latter will only be available if the system was compiled with support for cairo – otherwise "Xlib" will be used. The default is set by getOption("bitmapType") – the ‘out of the box’ default is "quartz" or "cairo" where available, otherwise "Xlib".
antialias for type = "cairo", giving the type of anti-aliasing (if any) to be used for fonts and lines (but not fills). See X11. The default is set by X11.options. Also for type = "quartz", where antialiasing is used unless antialias = "none".