最近用到的R

1，去掉背景

+theme(panel.grid.major =element_blank(),panel.grid.minor = element_blank(),panel.background = element_blank(),axis.line = element_line(colour = "black"))
2，

改变X轴标签

scale_x_discrete(
    breaks = c('Brain_inputRNAs.circ','Brain_m6aRNAs.circ'),
    label = c('circRNAs',~'m'~''^6*A~' circRNAs')

 

3，使X轴贴边

ggplot(newdata,aes(x=label,y=circ_num,fill=exon_num))+geom_area()+scale_x_continuous(limits = c(1,8),breaks = seq(1,8,1))+ylab('percentage')+scale_y_continuous(expand = c(0,0))+
+     coord_cartesian(ylim = c(0,100),expand = TRUE)

,4，上标以及下标

+scale_color_discrete(labels=c(~Log[10]~'(SRPTM+1)',~Log[2]~'m'~''^6*A~' abundance'))
5，删掉legend

+theme(legend.title=element_blank())

6，改变legend label顺序

scale_colour_discrete(name  ="Payer",
                            breaks=c("Female", "Male"),
                            labels=c("Woman", "Man")) ‘

7，给箱线图添加均值点

ggplot(dat, aes(x=cond, y=rating)) + geom_boxplot() +
    stat_summary(fun.y=mean, geom="point", shape=5, size=4)

8， 自定义fill的颜色
bp + scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"), 
                       name="Experimental\nCondition",
                       breaks=c("ctrl", "trt1", "trt2"),
                       labels=c("Control", "Treatment 1", "Treatment 2"))

#9，设置legend颜色和大小等
bp + theme(legend.text = element_text(colour="blue", size = 16, face = "bold"))
 

outlier.colour = NA

ggplot(newdata,aes(x=name,y=sample...1.))+
  geom_violin(fill='grey',width=.2)+geom_boxplot(width=.05,outlier.size = .5)+
  scale_y_continuous(limits = c(-14,2),breaks = seq(-14,2,2))+

10,将两个不同的legend合成一个：

+scale_color_discrete(name='Number of exons in'~m^6~'A circRNAs')+
  scale_fill_discrete(name='Number of exons in'~m^6~'A circRNAs')

11,将legend设置为一行

+guides(color = guide_legend(nrow = 1))

12，

Boxplot从下到上展示的是最小值，第一四分位数(箱子的下边线)、中位数(箱子中间的线)、第三四分位数(箱子上边线)、最大值，具体解读参见http://mp.weixin.qq.com/s/t3UTI_qAIi0cy1g6ZmHtwg。

13,

scale_x_discrete(limits=c("Jan 1997 - Aug 2003","Sep 2003 - Jun 2005","Jul 2005 - Dec 2009"),   expand=c(.08,0)) +

14，删除第二例

for i in `ls *.txt`
do
echo 'awk' "'"'{$2="" ; print $0}'"'" ${i} \>./out/${i} >>shanchu-dierlie.sh
done
15,

for i in `ls 3*.bed`
do
echo python chuyi-max-3-or-5.py ${i} 5-${i#3-*}  ./out/${i} >>chuyimax.sh
done