代码拉取完成，页面将自动刷新
#!/bin/bash
#set -x
usage()
{
cat <<EOF
${txtcyn}
***CREATED BY Chen Tong (chentong_biology@163.com)***
Usage:
$0 options${txtrst}
${bldblu}Function${txtrst}:
This script is used to draw histogram and density plot
for one column or multiple columns using ggplot2.
-------------------------------------------------------------
fileformat for -f, when -m is FALSE.
#Normal matrix with header lines
ctcf h3k27ac
1 2
1 3
4 2
1 5
6 7
0 10
fileformat for -f, when -m is true.
#The name "value" and "variable" shoud not be altered, but the order
#of this two columns is unlimited. Other columns will be ignored.
#Actually this format is the melted result of last format.
--------------------------------------------------------------
variable value set(optional)
h3k27ac 8.71298 1
h3k27ac 8.43246 1
h3k27ac 8.25497 1
h3k27ac 7.16265 1
h3k27ac 3.55341 1
h3k27ac 3.55030 2
h3k27ac 7.07502 2
h3k27ac 8.24328 2
h3k27ac 8.43869 2
h3k27ac 8.48877 2
ctcf 10.69130 1
ctcf 10.76680 1
ctcf 10.54410 1
ctcf 10.86350 1
ctcf 8.45751 1
ctcf 8.50316 2
ctcf 10.91430 2
ctcf 10.70220 2
ctcf 10.41010 2
ctcf 10.57570 2
-------------------------------------------------------------
${txtbld}OPTIONS${txtrst}:
-f Data file (with header line, the first column
will not be treated as rownames, tab seperated)${bldred}[NECESSARY]${txtrst}
-m When true, it will skip melt preprocesses. But the format must be
the same as listed before.
${bldred}[Default TRUE]${txtrst}
-M Lists of variables not want to be melted.
${bldred}[Only used when -m is FALSE, accept a string in
format like "'Set','Id'" meaning the 'Set' column and 'Id'
column will be retained as in original file.]${txtrst}
-d Plot frequency or density or hist or both frequency and
histogram[${txtred}Default <line> means frequency
accept <density_line>, <hist> or <both>${txtrst}]
-g Plot with density or count or frequency in
y-axis.[${txtred}Default <frequency>,
accept <..density..>, <..count..>.
When -d is <both>, <frequency> will be given here.${txtrst}]
-N Scale value. All values will be divided by supplied one.
Default 1.
-L The largest value allowed. Values other than this will be set as this value.
${bldred}[Default Inf]${txtrst}
-s Variable name for facet.[${txtred}Optional, the name of one
column representing a group should be given if group
information is needed. Here 'set' can be given if you want to
plot set-1 and set-2 separatelt ${txtrst}]
-J Another variable for facet.[${txtred}Optional, same meaning as
-s but different columns, like 'variable'. When this is given,
facet_grid would be used in format like facet_grid(s_facet ~
j_facet) pay attention to the order.]
-H Order of J_facet (facet variable given to -J).
[${txtred}Optional even -s is given. Only specified if the
facet order is what you want. Input format likes
"'facet1','facet2',"facet10""${txtrst}]
-S Number of columns in one row when do faceting.
${txtred}Necessary if only -s is given${txtrst}
-D Parameter for scales for facet.
[${txtred}Necessary if only -s is given. Default each inner
graph use same scale [x, y range]. "free", 'free_x', 'free_y'
is accepted.${txtrst}]
-G Order of s_facet (facet_variable given to -s).
[${txtred}Optional even -s is given. Only specified if the
facet order is what you want. Input format likes
"'facet1','facet2',"facet10""${txtrst}]
-j Position paramter for hist bars.[${txtred}Default identity,
accept <dodge>. ${txtrst}]
-k Alpha value for transparent.[${txtred}Default 0.4,
accept a number form 0 to 1, the smaller, the more
transparent. ${txtrst}]
-v Add mean value as vline.[${txtred}Default FALSE, accept
TRUE${txtrst}]
-l Levels for legend variable
[${txtred}Accept a string like "'ctcf','h3k27ac'".${txtrst}]
-P Legend position[${txtred}Default right. Accept
top,bottom,left,none, or c(0.08,0.8).${txtrst}]
-a The value for adjust (like the width of each bin) in geom_density.
and binwidth for geom_histogram)
[${txtred}Default ggplot2 default, accept a number${txtrst}]
-b Fill the area if TRUE.[${txtred}Default FALSE${txtrst}]
-X Display xtics. ${bldred}[Default TRUE]${txtrst}
-Y Display ytics. ${bldred}[Default TRUE]${txtrst}
-I Manually set xtics.${bldred}[Default FALSE, accept a series of
numbers in following format "c(1,2,3,4,5)" or other R code
that can generate a vector]${txtrst}
-W Manually set the value of xtics when -I is specified.
${bldred}[Default the content of -I when -I is specified,
accept a series of
numbers in following format "c(1,2,3,4,5)" or other R code
that can generate a vector to set the position of xtics]${txtrst}
-R Rotation angle for x-axis value(anti clockwise)
${bldred}[Default 0]${txtrst}
-V Add vline by given point.
${bldred}[Default FALSE, accept a series of
numbers in following format "c(1,2,3,4,5)" or other R code
that can generate a vector]${txtrst}
-A Add labels to vline.
${bldred}[Default FALSE, accept a series of
numbers in following format "c(1,2,3,4,5)" or other R code
that can generate a vector]${txtrst}
-B line size.[${txtred}Default 1. Accept a number.${txtrst}]
-t Title of picture[${txtred}Default empty title${txtrst}]
-x xlab of picture[${txtred}Default empty xlab${txtrst}]
-y ylab of picture[${txtred}Default empty ylab${txtrst}]
-c Manually set colors for each line.[${txtred}Default FALSE,
meaning using ggplot2 default.${txtrst}]
-C Color for each line.[${txtred}When -c is TRUE, str in given
format must be supplied, ususlly the number of colors should
be equal to the number of lines.
"'red','pink','blue','cyan','green','yellow'" or
"rgb(255/255,0/255,0/255),rgb(255/255,0/255,255/255),rgb(0/255,0/255,255/255),
rgb(0/255,255/255,255/255),rgb(0/255,255/255,0/255),rgb(255/255,255/255,0/255)"
${txtrst}]
-p Other legal R codes for gggplot2 will be given here.
[${txtres}Begin with '+' ${txtrst}]
-w The width of output picture.[${txtred}Default 20${txtrst}]
-u The height of output picture.[${txtred}Default 12${txtrst}]
-E The type of output figures.[${txtred}Default pdf, accept
eps/ps, tex (pictex), png, jpeg, tiff, bmp, svg and wmf)${txtrst}]
-r The resolution of output picture.[${txtred}Default 300 ppi${txtrst}]
-z Is there a header[${bldred}Default TRUE${txtrst}]
-e Execute or not[${bldred}Default TRUE${txtrst}]
-i Install depended packages[${bldred}Default FALSE${txtrst}]
EOF
}
file=
title=''
melted='TRUE'
type_p='line'
type_hist='..count../sum(..count..)'
vline='FALSE'
xlab='NULL'
ylab='NULL'
level=""
x_level=""
xvariable=
x_type='TRUE'
scaleY='FALSE'
adjust='FALSE'
fill_area='FALSE'
header='TRUE'
execute='TRUE'
ist='FALSE'
uwid=20
vhig=12
res=300
ext='pdf'
par=''
legend_pos='right'
smooth='FALSE'
smooth_method='auto'
line_size=1
xtics='TRUE'
alpha=0.4
xtics_angle=0
ytics='TRUE'
color='FALSE'
color_v=''
pos="identity"
scale=1
xtics_input=0
xtics_value=0
custom_vline='NULL'
custom_vanno='NULL'
facet='haha'
facet_ncol=1
facet_order=''
facet_scale='fixed'
j_facet='haha'
j_facet_order=''
largest='Inf'
while getopts "hf:m:M:N:t:a:x:b:l:D:d:V:A:g:G:j:J:H:I:W:L:k:P:y:c:C:B:X:Y:R:s:S:w:u:r:E:p:z:v:e:i:" OPTION
do
case $OPTION in
h)
usage
exit 1
;;
f)
file=$OPTARG
;;
m)
melted=$OPTARG
;;
M)
xvariable=$OPTARG
;;
V)
custom_vline=$OPTARG
;;
A)
custom_vanno=$OPTARG
;;
N)
scale=$OPTARG
;;
t)
title=$OPTARG
;;
G)
facet_order=$OPTARG
;;
D)
facet_scale=$OPTARG
;;
S)
facet_ncol=$OPTARG
;;
s)
facet=$OPTARG
;;
J)
j_facet=$OPTARG
;;
L)
largest=$OPTARG
;;
H)
j_facet_order=$OPTARG
;;
a)
adjust=$OPTARG
;;
I)
xtics_input=$OPTARG
;;
W)
xtics_value=$OPTARG
;;
d)
type_p=$OPTARG
;;
g)
type_hist=$OPTARG
;;
v)
vline=$OPTARG
;;
b)
fill_area=$OPTARG
;;
x)
xlab=$OPTARG
;;
l)
level=$OPTARG
;;
j)
pos=$OPTARG
;;
k)
alpha=$OPTARG
;;
P)
legend_pos=$OPTARG
;;
B)
line_size=$OPTARG
;;
c)
color=$OPTARG
;;
C)
color_v=$OPTARG
;;
X)
xtics=$OPTARG
;;
R)
xtics_angle=$OPTARG
;;
Y)
ytics=$OPTARG
;;
p)
par=$OPTARG
;;
y)
ylab=$OPTARG
;;
w)
uwid=$OPTARG
;;
u)
vhig=$OPTARG
;;
r)
res=$OPTARG
;;
E)
ext=$OPTARG
;;
z)
header=$OPTARG
;;
e)
execute=$OPTARG
;;
i)
ist=$OPTARG
;;
?)
usage
exit 1
;;
esac
done
if [ -z $file ]; then
usage
exit 1
fi
mid='.densityHist'
cat <<END >${file}${mid}.r
if ($ist){
install.packages("ggplot2", repo="http://cran.us.r-project.org")
install.packages("reshape2", repo="http://cran.us.r-project.org")
install.packages("grid", repo="http://cran.us.r-project.org")
install.packages("plyr", repo="http://cran.us.r-project.org")
}
library(ggplot2)
library(reshape2)
library(grid)
if (${vline}){
library(plyr)
}
if(! $melted){
#cat("Currently not supported for unmelted files")
#quit()
#currently this part is unused
data <- read.table(file="${file}", sep="\t", header=$header, quote="")
# data_rownames <- rownames(data)
# data_colnames <- colnames(data)
# data\$${xvariable} <- data_rownames
data_m <- melt(data, id.vars=c(${xvariable}))
#data_m <- melt(data)
} else {
data_m <- read.table(file="$file", sep="\t",
header=$header, quote="")
}
if(${scale} != 1) {
data_m\$value <- data_m\$value/${scale}
}
level_i <- c(${level})
if (length(level_i) > 1){
data_m\$variable <- factor(data_m\$variable, levels=level_i)
}
#else if (! ${melted}){
# data_m\$variable <- factor(data_m\$variable, levels=data_colnames,
# ordered=T)
#}
facet_order_i <- c(${facet_order})
if (length(facet_order_i) > 1){
data_m\$${facet} <- factor(data_m\$${facet},
levels=facet_order_i)
}
j_facet_order_i <- c(${j_facet_order})
if (length(j_facet_order_i) > 1){
data_m\$${j_facet} <- factor(data_m\$${j_facet},
levels=j_facet_order_i)
}
data_m\$value[data_m\$value>$largest] <- $largest
p <- ggplot(data_m, aes(x=value))
if ("${type_p}"=="hist" || "${type_p}"=="both"){
#if ("${type_p}" == "both" || "${type_hist}" == "density"){
if (${adjust}){
p <- p + geom_histogram(aes(y=${type_hist},
fill=variable), binwidth=${adjust}, alpha=${alpha},
position="${pos}")
} else {
p <- p + geom_histogram(aes(y=${type_hist},
fill=variable), alpha=${alpha}, position="${pos}")
}
#} else {
# if (${adjust}){
# p <- p + geom_histogram(alpha=${alpha}, aes(fill=variable),
# binwidth=${adjust}, position="${pos}")
# } else {
# p <- p + geom_histogram(alpha=${alpha}, aes(fill=variable),
# position="${pos}")
# }
#}
}
if ("${type_p}"=="density_line"){
if (${fill_area} && "${type_p}" != "both"){
if (${adjust}){
p <- p + geom_density(size=${line_size}, alpha=${alpha},
aes(fill=variable, y=${type_hist}), adjust=${adjust})
}
p <- p + geom_density(size=${line_size}, alpha=${alpha},
aes(fill=variable), y=${type_hist})
} else {
if (${adjust}){
p <- p + stat_density(adjust=${adjust}, size=${line_size},
aes(color=variable, group=variable, y=${type_hist}), geom="line",
position="identity")
} else {
p <- p + stat_density(size=${line_size},
aes(color=variable, group=variable, y=${type_hist}), geom="line",
position="identity")
}
}
}
if ("${type_p}"=="line" || "${type_p}"=="both"){
#if (${fill_area} && "${type_p}" != "both"){
if (${adjust}){
p <- p + geom_freqpoly(size=${line_size}, alpha=${alpha},
aes(color=variable, y=${type_hist}), binwidth=${adjust})
}else{
p <- p + geom_freqpoly(size=${line_size}, alpha=${alpha},
aes(color=variable, y=${type_hist}))
}
#} else {
# if (${adjust}){
# p <- p + stat_density(adjust=${adjust}, size=${line_size},
# aes(color=variable, group=variable, y=${type_hist}), geom="line",
# position="identity")
# } else {
# p <- p + stat_density(size=${line_size},
# aes(color=variable, group=variable, y=${type_hist}), geom="line",
# position="identity")
# }
#}
}
if (${vline}){
cdf <- ddply(data_m, .(variable), summarise, rating.mean=mean(value))
p <- p + geom_vline(data=cdf, aes(xintercept=rating.mean,
colour=variable),linetype="dashed", size=1)
}
p <- p + xlab("$xlab") + ylab("$ylab") + theme_bw() +
theme(legend.title=element_blank(),
panel.grid.major = element_blank(), panel.grid.minor = element_blank())
p <- p + theme(axis.ticks.x = element_blank(), legend.key=element_blank())
#legend.background = element_rect(fill = "white"), legend.box=NULL,
#legend.margin=unit(0,"cm"))
#if ("${line_size}" != ""){
# p <- p + geom_line(size=${line_size})
#}else{
# p <- p + geom_line()
#}
if(${color}){
if (${fill_area}){
p <- p + scale_fill_manual(values=c(${color_v}))
} else {
p <- p + scale_color_manual(values=c(${color_v}))
}
}
if ("${j_facet}" != "haha") {
p <- p + facet_grid(${facet} ~ ${j_facet}, scales="${facet_scale}")
}else {
if ("${facet}" != "haha") {
p <- p + facet_wrap(~${facet}, ncol=${facet_ncol},
scales="${facet_scale}")
}
}
if ("$xtics" == "FALSE"){
p <- p + theme(axis.text.x=element_blank())
}else{
if (${xtics_angle} != 0){
p <- p + theme(axis.text.x=element_text(angle=${xtics_angle},hjust=1))
}
}
if ("$ytics" == "FALSE"){
p <- p + theme(axis.text.y=element_blank())
}
top='top'
botttom='bottom'
left='left'
right='right'
none='none'
legend_pos_par <- ${legend_pos}
p <- p + theme(legend.position=legend_pos_par)
xtics_v <- ${xtics_input}
xtics_value <- ${xtics_value}
if(length(xtics_v) > 1){
if(length(xtics_value)<=1){
xtics_value <- xtics_v
}
p <- p + scale_x_continuous(breaks=xtics_v, labels=xtics_value)
}
custom_vline_coord <- ${custom_vline}
custom_vline_anno <- ${custom_vanno}
if(is.vector(custom_vline_coord)){
p <- p + geom_vline(xintercept=custom_vline_coord,
linetype="dotted")
if(is.vector(custom_vline_anno)){
ymax_range <- ggplot_build(p)\$panel\$ranges[[1]]\$y.range
ymax_v <- ymax_range[2]
p <- p + annotate("text", x=custom_vline_coord, y=ymax_v,
label=custom_vline_anno, hjust=0)
}
}
p <- p${par}
ggsave(p, filename="${file}${mid}.${ext}", dpi=$res, width=$uwid,
height=$vhig, units=c("cm"))
#png(filename="${file}${mid}.png", width=$uwid, height=$vhig,
#res=$res)
#p
#dev.off()
END
if [ "$execute" == "TRUE" ]; then
Rscript ${file}${mid}.r
if [ "$?" == "0" ]; then /bin/rm -f ${file}${mid}.r; fi
fi
此处可能存在不合适展示的内容，页面不予展示。您可通过相关编辑功能自查并修改。
如您确认内容无涉及 不当用语 / 纯广告导流 / 暴力 / 低俗色情 / 侵权 / 盗版 / 虚假 / 无价值内容或违法国家有关法律法规的内容，可点击提交进行申诉，我们将尽快为您处理。