参考：zhuanlan.zhihu.com/p/27162794
www.cookbook-r.com/Graphs/Output_to_a_file/
blog.sciencenet.cn/blog-306699-1027071.html
实例：以下是JCI杂志的图片要求
---
JCI
Figure instructions for acceptedmanuscripts
https://jci.org/kiosks/publish/figures#General_requirements
·Entire figure is set at 17.8 cm and 600 ppi
·Color panel is 3 cm wide
·Text is labeled in8 pt Helvetica/ Arial
·Minimum resolution: all images 600 pixels perinch (ppi)
No Drop shadows
No labels over color photograph panels, if possible
No pairing red and green in graphs to ensure legibility for colorblind readers
Formats of figure
file: TIFF (tagged image file format) is best, but we can accept PowerPoint, high-resolution PDF, EPS, and Illustrator files. But no Canvas or Corel Draw files.
---
以下是一个postdoc给我的建议
A free software Inkscape (https://inkscape.org/en/) to replace Illustrator. he prefer the raw figure to be output as vector format (eg. .SVG, .EMF, instead of raster format, eg. JPEG, TIFF, PNG, BMP, etc) because it can be scaled infinitely without losing quality. he suggests preparing the sub-figures individually from various sources (IGV, power point, etc), import them in Inkscape, scale and arrange, and export as TIFF with enough resolution.
要知道一个单位换算：1in=2.54cm=25.4mm=72pt=6pc
后来我发现也可以直接从Rstudio输出600dpi，8 ptHelvetica/ Arial的Tiff图片，尺寸（图片的宽要小于 17cm （6.69in）当只放一个的时候，两个的时候就差不多8cm=3.14in左右）也可以设定。然后input到incscape里，也是一个好办法，因为figure ligent要求8 ptHelvetica/ Arial。还有一般杂志还有要求长度不可以超过3/4page（17.25cm=6.8in）。这里的page指的是A4纸，A4纸尺寸：210mm × 297mm（=8.27in x 11.69in）
1. 那么根据以上的信息，我们可以用Rstudio直接export tiff 格式的图片（sub-figure）。
---
tiff("Fig 2 MDplot.tif", height = 2, width = 3,units="in", res=600, family = "Arial”, pointsize=8)
op <- par(mar = c(5, 4, 2, 2) + 0.1)
plotMD(tr, status=is.de, values=c(1,-1), col=c("red","blue"),legend=FALSE, main=TRUE)
par(op)
dev.off()
---
tiff("Fig 2 PCA.tif", height = 2, width = 3.2,units="in", res=600,family = "Arial", pointsize=8)
op <- par(mar = c(5, 4, 0.05, 0.05) + 0.1)
p=ggplot(Data_frame,aes(PC1,PC2))
print(
p+geom_point(size=1,alpha=1,aes(color=group))+geom_text(aes(label = type), hjust=0.5, vjust=0,size=1.5)+
theme(axis.title.x =element_text(family="Arial",size=8), axis.title.y =element_text(family="Arial",size=8),axis.text.x=element_text(family = "Arial",size=8),axis.text.y=element_text(family = "Arial",size=8),legend.text=element_text(family = "Arial",size=8))
)
par(op)
dev.off()
---
tiff("Fig 2 cluser Dendrogram.tif", height = 2, width = 3.4,units="in", res=600,family = "Arial", pointsize=8)
op <- par(mar = c(3, 4, 1, 1) + 0.1)
print(myplclust(ward.hclust, labels=colnames(q.f.cpm),main= "",lab.col=as.fumeric(g)))
par(op)
dev.off()
---
2. Tiff 600dpi 的sub-figure inport到incscape
尺寸就是2in x 3in，分辨率 600dpi，字体Arial，字号8pt。 JC要求全是非粗体，有些R package出来的Main tittle默认就是粗体，而且也不知道怎么改变，我就在incscape里加上title。还有一点要注意，inport 到 incscape里的图一开始会犹豫分别率太高（600dpi）而被自动放大，（面积大了dpi就小了），不要担心，进去后，再把刚刚inport的图片尺寸调节一下就复原到了之前的dpi了，字号也是8pt了。在incscape里自己设计组装每个sub-figure，每个main figure 一个inscape 文件。
