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#!/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 a line or multiple lines using ggplot2.
You can specify whether or not smooth your line or lines.
Two types of input files are supported, normal matrix or melted matrix format. Column separator for both types of input files is **tab**.
Here is an example of normal matrix format. The first column will be treated as X-axis variables and other columns represents each type of lines. The number of columns is unlimited and names of columns is unlimited.
**Set** column is not needed. If given, <facet_plot> (multiple plots in one page) could be displayed.
------------------------------------------------------------
Pos H3K27ac CTCF Enhancer H3K4me3 polII
-5000 8.71298 10.69130 11.7359 10.02510 8.26866
-4000 8.43246 10.76680 11.8442 9.76927 7.78358
-3000 8.25497 10.54410 12.2470 9.40346 6.96859
-2000 7.16265 10.86350 12.6889 8.35070 4.84365
-1000 3.55341 8.45751 12.8372 4.84680 1.26110
0 3.55030 8.50316 13.4152 5.17401 1.50022
1000 7.07502 10.91430 12.3588 8.13909 4.88096
2000 8.24328 10.70220 12.3888 9.47255 7.67968
3000 8.43869 10.41010 11.9760 9.80665 7.94148
4000 8.48877 10.57570 11.6562 9.71986 8.17849
------------------------------------------------------
------------With SET------------------------------------------
Pos H3K27ac CTCF Enhancer H3K4me3 polII Set
-5000 8.71298 10.69130 11.7359 10.02510 8.26866 1
-4000 8.43246 10.76680 11.8442 9.76927 7.78358 1
-3000 8.25497 10.54410 12.2470 9.40346 6.96859 1
-2000 7.16265 10.86350 12.6889 8.35070 4.84365 1
-1000 3.55341 8.45751 12.8372 4.84680 1.26110 1
0 3.55030 8.50316 13.4152 5.17401 1.50022 1
1000 7.07502 10.91430 12.3588 8.13909 4.88096 1
2000 8.24328 10.70220 12.3888 9.47255 7.67968 1
3000 8.43869 10.41010 11.9760 9.80665 7.94148 1
4000 8.48877 10.57570 11.6562 9.71986 8.17849 1
-5000 8.71298 10.69130 11.7359 10.02510 8.26866 2
-4000 8.43246 10.76680 11.8442 9.76927 7.78358 2
-3000 8.25497 10.54410 12.2470 9.40346 6.96859 2
-2000 7.16265 10.86350 12.6889 8.35070 4.84365 2
-1000 3.55341 8.45751 12.8372 4.84680 1.26110 2
0 3.55030 8.50316 13.4152 5.17401 1.50022 2
1000 7.07502 10.91430 12.3588 8.13909 4.88096 2
2000 8.24328 10.70220 12.3888 9.47255 7.67968 2
3000 8.43869 10.41010 11.9760 9.80665 7.94148 2
4000 8.48877 10.57570 11.6562 9.71986 8.17849 2
-------------------------------------------------------------
For matrix format, example command lines include:
* Attribute of X-axis value (first column of matrix) is <number>
s-plot lines -f matrix.file -A FALSE
* Attribute of X-axis value (first column of matrix) is <text>
s-plot lines -f matrix.file
* Attribute of X-axis value (first column of matrix) is numbers, change legned order (default alphabet order)
s-plot lines -f matrix.file -l "'polII', 'CTCF', 'Enhancer', 'H3K27ac', 'H3K4me3'"
* Attribute of X-axis value (first column of matrix) is numbers, change legned order (default alphabet order), smooth lines to look better (Pay attention to whether this will change the data trend)
s-plot lines -f matrix.file -l "'polII', 'CTCF', 'Enhancer', 'H3K27ac', 'H3K4me3'" -o TRUE
* Attribute of X-axis value (first column of matrix) is numbers, with <Set> (Set is column name) column
s-plot lines -f matrix.file -F "+facet_grid(Set ~ ., scale='free_y')"
FILEFORMAT when -m is true
#The name "value" shoud **not** be altered.
#variable can be altered using -H
#Actually this format is the melted result of last format.
--------------------------------------------------------------
Pos variable value
-5000 H3K27ac 8.71298
-4000 H3K27ac 8.43246
-3000 H3K27ac 8.25497
-2000 H3K27ac 7.16265
-1000 H3K27ac 3.55341
0 H3K27ac 3.55030
1000 H3K27ac 7.07502
2000 H3K27ac 8.24328
3000 H3K27ac 8.43869
4000 H3K27ac 8.48877
-5000 CTCF 10.69130
-4000 CTCF 10.76680
-3000 CTCF 10.54410
-2000 CTCF 10.86350
-1000 CTCF 8.45751
0 CTCF 8.50316
1000 CTCF 10.91430
2000 CTCF 10.70220
3000 CTCF 10.41010
4000 CTCF 10.57570
-------------------------------------------------------------
* Attribute of X-axis value (melt format) is <number>
s-plot lines -f matrix.file -m TRUE -a Pos -A FALSE
* Attribute of X-axis value (first column of matrix) is <text>
s-plot lines -f matrix.file -m TRUE -a Pos
* If the name of the second column is <type> not <variable>, one should specify with <-H>.
s-plot lines -f matrix.file -A FALSE -m TRUE -a Pos -H type
* Attribute of X-axis value (first column of matrix) is numbers, change legned order (default alphabet order)
s-plot lines -f matrix.file -m TRUE -a Pos -l "'polII', 'CTCF', 'Enhancer', 'H3K27ac', 'H3K4me3'"
* Attribute of X-axis value (first column of matrix) is numbers, change legned order (default alphabet order), smooth lines to look better (Pay attention to whether this will change the data trend)
s-plot lines -f matrix.file -m TRUE -a Pos -l "'polII', 'CTCF', 'Enhancer', 'H3K27ac', 'H3K4me3'" -o TRUE
* Attribute of X-axis value (first column of matrix) is numbers, with <Set> (Set is column name) column
s-plot lines -f matrix.file -F "+facet_grid(Set ~ ., scale='free_y')"
${txtbld}OPTIONS${txtrst}:
-f Data file (with header line, the first column would be be treated as rownames for
normal matrix. No rownames for melted format. Columns are tab seperated)
${bldred}[NECESSARY]${txtrst}
-m When true, it will skip melt preprocesses. But the format must be
the same as listed before.
${bldred}[Default FALSE, accept TRUE]${txtrst}
-a Name for x-axis variable
[${txtred}Only needed when <-m> is <TRUE>.
For the melted data, 'Pos' should be given here.
For normal matrix, default the first column will be used,
program will assign an value 'xvariable' to represent it.
]${txtrst}]
-A Are x-axis variables numbers.
[${txtred}Default <TRUE>, meaning X-axis label is <text>.
<FALSE> means X-axis label is <numerical>.${txtrst}]
-H Name for legend variable.
${bldred}[Default variable, this should only be set when -m is TRUE]${txtrst}
-J Name for color variable.
${bldred}[Default same as -H, this should only be set when -m is TRUE]${txtrst}
-l Set orders of legend variable.
[${txtred}Default column order for normal matrix, accept a string like
"'CTCF','H3K27ac','Enhancer'" to set your own order.
Pay attention to the usage of two types of quotes.
***When -m is TRUE, default order would be alphabet order.*********
${txtrst}]
-P Legend position[${txtred}Default right. Accept
top, bottom, left, none, or 'c(0.08,0.8)'.${txtrst}]
-L Levels for x-axis variable, suitable when x-axis is not treated as numerical.
[${txtred}Default the order of first column for normal matrix.
Accept a string like "'g','a','j','x','s','c','o','u'" to set your own oder.
This will only be considered when -A is TRUE.
***When -m is used, this default order would be alphabet order.*********
${txtrst}]
-o Smooth lines or not.
[${txtred}Default FALSE means no smooth. Accept TRUE to smooth lines.${txtrst}]
-O The smooth method you want to use.
[${txtred}smoothing method (function) to use, eg. lm, glm, gam, loess,rlm.
For datasets with n < 1000 default is 'loess'.
For datasets with 1000 or more observations defaults to 'gam'.
${txtrst}]
-V Add vertical lines.${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}
-D Add labels to vlines.
${bldred}[Default same as -V.
Accept a series of numbers in following format "c(1,2,3,4,5)" or other R code
that can generate a vector as labels.
Or one can give '1' to disallow labels]${txtrst}
-j Add horizontal lines.${bldred}[Default FALSE, accept a series of
numbers in following format "c(1,2,3,4,5)" or other
R code that can generate a vector]${txtrst}
-d Add labels to hline.
${bldred}[Default same as -j
Accept a series of numbers in following format "c(1,2,3,4,5)" or other R code
that can generate a vector as labels.
Or one can give '1' to disallow labels]${txtrst}
-I Manually set the position of xtics.
${bldred}[Default FALSE, accept a series of
numbers in following format "c(1,2,3,4,5)" or other R code
that can generate a vector to set the position of xtics]${txtrst}
-b 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}
-X Display xtics. ${bldred}[Default TRUE]${txtrst}
-Y Display ytics. ${bldred}[Default TRUE]${txtrst}
-R Rotation angle for x-axis labels (anti clockwise)
${bldred}[Default 0]${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, one has two options:
1. Supplying a function to generate colors,
like "rainbow(11)" or "rainbow(11, alpha=0.6)",
rainbow is an R color palletes,
11 is the number of colors you want to get,
0.6 is the alpha value.
The R palletes include <heat.colors>, <terrain.colors>,
<topo.colors>, <cm.colors>.
2. Supplying a list of colors in given format,
the number of colors should be equal to the number of
bars like "'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)"
${txtrst}
One can use R fucntion <colors()> to list all available colors.
-s Scale y axis
[${txtred}Default null. Accept TRUE. This function is depleted.
But if the supplied number after -S is not 0, this parameter will be set to TRUE${txtrst}]
-F The formula for facets.[${bldred}Default no facets,
"+facet_grid(level ~ .)" means divide by levels of 'level' vertically.
"+facet_grid(. ~ level)" means divide by levels of 'level' horizontally.
"+facet_grid(lev1 ~ lev2)" means divide by lev1 vertically and lev2 horizontally.
"+facet_wrap(~level, ncol=2)" means wrap horizontally with 2 columns.
#Pay attention to the single quote for parameters in function for scale.
Example: "+facet_wrap(~Size,ncol=6,scale='free')"
Example: "+facet_grid(Size ~ .,scale='free_y')"
${txtrst}]
-G If facet is given, you may want to specifize the order of
variable in your facet, default alphabetical order.
[${txtred}Accept sth like (one level one sentence, separate by';')
'data\$size <- factor(data\$size, levels=c("l1", "l2",...,"l10"), ordered=T)' ${txtrst}]
-v If scale is TRUE, give the following 'scale_y_log10()'[default], 'coord_trans(y="log10")',
or other legal command for ggplot2 or simply 'log2'.${txtrst}]
-S A number to add if scale is used.
[${txtred}Default 0. If a non-zero number is given, -s would be set to TRUE.${txtrst}]
-p Other legal R codes for gggplot2 could be given here.
[${txtres}Begin with '+' ${txtrst}]
-w The width of output picture (cm).[${txtred}Default 20${txtrst}]
-u The height of output picture (cm).[${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${txtrst}]
-z Is there a header. Must be TRUE. [${bldred}Default TRUE${txtrst}]
-e Execute or not[${bldred}Default TRUE${txtrst}]
-i Install depended packages[${bldred}Default FALSE${txtrst}]
EOF
}
file=
title=''
melted='FALSE'
xlab=''
ylab=''
xvariable='xvariable'
variable='variable'
color_variable='variable'
level=""
x_level=""
x_type='TRUE'
scaleY='FALSE'
y_add=0
scaleY_x='scale_y_log10()'
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'
xtics_angle=0
ytics='TRUE'
color='FALSE'
color_v=''
custom_vline='NULL'
custom_vanno='NULL'
custom_hline='NULL'
custom_hanno='NULL'
facet=''
facet_o=''
xtics_pos=0
xtics_value=0
while getopts "hf:m:a:A:b:I:t:x:l:j:J:d:F:G:H:P:L:y:V:D:c:C:B:X:Y:R:w:u:r:o:O:s:S:p:z:v:e:E:i:" OPTION
do
case $OPTION in
h)
usage
exit 1
;;
f)
file=$OPTARG
;;
m)
melted=$OPTARG
;;
a)
xvariable=$OPTARG
;;
A)
x_type=$OPTARG
;;
H)
variable=$OPTARG
;;
V)
custom_vline=$OPTARG
;;
D)
custom_vanno=$OPTARG
;;
j)
custom_hline=$OPTARG
;;
J)
color_variable=$OPTARG
;;
d)
custom_hanno=$OPTARG
;;
I)
xtics_pos=$OPTARG
;;
b)
xtics_value=$OPTARG
;;
t)
title=$OPTARG
;;
x)
xlab=$OPTARG
;;
l)
level=$OPTARG
;;
F)
facet=$OPTARG
;;
G)
facet_o=$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=$OPTARG
;;
L)
x_level=$OPTARG
;;
p)
par=$OPTARG
;;
y)
ylab=$OPTARG
;;
w)
uwid=$OPTARG
;;
u)
vhig=$OPTARG
;;
r)
res=$OPTARG
;;
E)
ext=$OPTARG
;;
o)
smooth=$OPTARG
;;
O)
smooth_method=$OPTARG
;;
s)
scaleY=$OPTARG
;;
S)
y_add=$OPTARG
;;
v)
scaleY_x=$OPTARG
;;
z)
header=$OPTARG
;;
e)
execute=$OPTARG
;;
i)
ist=$OPTARG
;;
?)
usage
exit 1
;;
esac
done
if [ -z $file ]; then
usage
exit 1
fi
if test ${y_add} -ne 0; then
scaleY="TRUE"
fi
if test "${color_variable}" == "variable"; then
color_variable=${variable}
fi
mid='.lines'
if test "${smooth}" == 'TRUE'; then
mid=${mid}'.smooth'
fi
cat <<END >${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")
}
library(ggplot2)
library(reshape2)
library(grid)
if(! $melted){
data <- read.table(file="${file}", sep="\t", header=$header,
row.names=1, check.names=F, quote="")
data_rownames <- rownames(data)
data_colnames <- colnames(data)
data\$${xvariable} <- data_rownames
data_m <- melt(data, id.vars=c("${xvariable}"))
} else {
data_m <- read.table(file="$file", sep="\t",
header=$header, check.names=F, quote="")
}
if (${y_add} != 0){
data_m\$value <- data_m\$value + ${y_add}
if ("${scaleY_x}" == "log2") {
data_m\$value <- log2(data_m\$value)
}
}
if ("${level}" != ""){
level_i <- c(${level})
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)
}
#if (${x_type}){
# if ("${x_level}" != ""){
# x_level <- c(${x_level})
# data_m\$${xvariable} <- factor(data_m\$${xvariable},levels=x_level)
# } else if(! $melted){
# data_m\$${xvariable} <- factor(data_m\$${xvariable},levels=data_rownames,ordered=TRUE)
# }
#}
if ("${x_level}" != ""){
x_level <- c(${x_level})
data_m\$${xvariable} <- factor(data_m\$${xvariable},levels=x_level)
} else if(! $melted){
data_m\$${xvariable} <- factor(data_m\$${xvariable},levels=data_rownames,ordered=TRUE)
}
if ((! ${x_type}) & (! ${melted})){
data_m\$${xvariable} <-
as.numeric(levels(data_m\$${xvariable}))[data_m\$${xvariable}]
}
#if(! ${color}){
# data_m\$${variable} <-
# as.numeric(levels(data_m\$${variable}))[data_m\$${variable}]
#}
${facet_o}
p <- ggplot(data_m, aes(x=$xvariable, y=value, color=${color_variable},
group=${variable})) +
xlab("$xlab") + ylab("$ylab") + theme_bw() + labs(title="${title}") +
theme(legend.title=element_blank(),
panel.grid.major = element_blank(), panel.grid.minor = element_blank())
p <- p + expand_limits(y = 0)
#p <- p + scale_y_continuous(expand=c(0, 0))
p <- p + theme(legend.key=element_blank())
#legend.background = element_rect(colour='white'))
#legend.background = element_rect(fill = "white"), legend.box=NULL,
#legend.margin=unit(0,"cm"))
if (${smooth}){
if ("${line_size}" != ""){
p <- p + stat_smooth(method="${smooth_method}", se=FALSE,
size=${line_size})
}else{
p <- p + stat_smooth(method="${smooth_method}", se=FALSE,
size=${line_size})
}
}else{
if ("${line_size}" != ""){
p <- p + geom_line(size=${line_size}, alpha=0.6)
}else{
p <- p + geom_line(alpha=0.6)
}
}
if($scaleY & ("$scaleY_x" != "log2")){
p <- p + $scaleY_x
}
if(${color}){
p <- p + scale_color_manual(values=c(${color_v}))
}
#else {
#p <- p + scale_colour_brewer()
#p <- p + scale_colour_discrete(limits=levels(data_m\$${variable}),
#breaks=unique(data_m\$${variable}))
#}
if ("$xtics" == "FALSE"){
p <- p + theme(axis.text.x=element_blank(), axis.ticks.x = element_blank())
}else{
if (${xtics_angle} != 0){
if (${xtics_angle} == 90){
p <- p + theme(axis.text.x=
element_text(angle=${xtics_angle},hjust=1, vjust=0.5))
}else if (${xtics_angle} == 45){
p <- p + theme(axis.text.x=
element_text(angle=${xtics_angle},hjust=1, vjust=1))
} else {
p <- p + theme(axis.text.x=
element_text(angle=${xtics_angle},hjust=0.5, vjust=0.5))
}
}
}
if ("$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_pos <- ${xtics_pos}
xtics_value <- ${xtics_value}
if(length(xtics_pos) > 1){
if(length(xtics_value) <= 1){
xtics_value <- xtics_pos
}
p <- p + scale_x_continuous(breaks=xtics_pos, labels=xtics_value)
}
#custom_vline_coord <- ${vline}
#if(length(custom_vline_coord) > 1){
# p <- p + geom_vline(xintercept=custom_vline_coord,
# linetype="dotted" )
#}
custom_vline_coord <- ${custom_vline}
custom_vline_anno <- ${custom_vanno}
if ("${custom_vanno}" == "NULL" ){
custom_vline_anno <- custom_vline_coord
}
if(is.vector(custom_vline_coord)){
p <- p + geom_vline(xintercept=custom_vline_coord,
linetype="dotted", size=0.5)
if(is.vector(custom_vline_anno)){
#ymax_range <- ggplot_build(p)\$panel\$ranges[[1]]\$y.range
#ymax_v <- ymax_range[2]
ymax_v <- max(data_m\$value)
if ("${facet}" != ""){
ymax_v = 0
}
p <- p + annotate("text", x=custom_vline_coord, y=ymax_v,
label=custom_vline_anno, hjust=0)
}
}
custom_hline_coord <- ${custom_hline}
custom_hline_anno <- ${custom_hanno}
if ("${custom_hanno}" == "NULL" ){
custom_hline_anno <- custom_hline_coord
}
if(is.vector(custom_hline_coord)){
p <- p + geom_hline(yintercept=custom_hline_coord,
linetype="dotted", size=0.5)
if(is.vector(custom_hline_anno)){
#xmax_range <- ggplot_build(p)\$panel\$ranges[[1]]\$x.range
#xmax_v <- xmax_range[2]
#if ("${facet}" != ""){
# xmax_v = 0
#}
p <- p + annotate("text", y=custom_hline_coord, x=0,
label=custom_hline_anno, vjust=0, hjust=0)
}
}
p <- p ${facet}
p <- p${par}
#png(filename="${file}${mid}.png", width=$uwid, height=$vhig,
#res=$res)
ggsave(p, filename="${file}${mid}.${ext}", dpi=$res, width=$uwid,
height=$vhig, units=c("cm"))
#postscript(file="${file}${mid}.eps", onefile=FALSE, horizontal=FALSE,
#paper="special", width=10, height = 12, pointsize=10)
#dev.off()
END
if [ "$execute" == "TRUE" ]; then
Rscript ${file}${mid}.r
if [ "$?" == "0" ]; then /bin/rm -f ${file}${mid}.r; fi
fi
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