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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 specifially for output of
count_features_given_MIN_FPKM_threshold.pl.
${txtbld}OPTIONS${txtrst}:
-f Data file (with header line, the first column is the
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.
${bldred}[Default FALSE, accept TRUE]${txtrst}
-a Name for x-axis variable
[${txtred}Necessary, no default value when -m is used.
For the second examples, 'Pos' should be given here.
For the first example, default the first column will be used,
program will assign an value 'xvariable' to represent it.
]${txtrst}]
-A The attribute of x-axis variable.
[${txtred}Default TRUE, means X-axis label is text.
FALSE means X-axis label is number.${txtrst}]
-l Levels for legend variable
[${txtred}Default column order, accept a string like
"'ctcf','h3k27ac','enhancer'"
***When -m is used, this default will be ignored too.*********
${txtrst}]
-P Legend position[${txtred}Default right. Accept
top,bottom,left,none, or c(0.08,0.8).${txtrst}]
-L Levels for x-axis variable, suitable when x-axis is not used
as a number.
[${txtred}Default the order of first column, accept a string like
"'g','a','j','x','s','c','o','u'"
This will only be considered when -A is TRUE.
***When -m is used, this default will be ignored too.*********
${txtrst}]
-o Smooth your data or not.
[${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}
-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 value(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 have 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,
ususlly 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)"
${txtrst}]
-s Scale y axis
[${txtred}Default null. Accept TRUE. This function is
depleted. If the supplied number after -S is not 0, this
parameter is TRUE${txtrst}]
-F The formula for facets.[${bldred}Default no facets,
+facet_grid(level ~ .) means divide by levels of 'level' vertcally.
+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.
Example: +facet_wrap(~Size,ncol=6,scale='free')
${txtrst}]
-G If facet is given, you may want to specifize the order of
variable in your facet, default alphabetically.
[${txtred}Accept sth like
(one level one sentence, separate by';')
data\$size <- factor(data\$size, levels=c("l1",
"l2",...,"l10"), ordered=T) ${txtrst}]
-v If scale is TRUE, give the following
scale_y_log10()[default], coord_trans(y="log10"), or other legal
command for ggplot2)${txtrst}]
-S A number to add if scale is used.
[${txtred}Default 0. If a non-zero number is given, -s is
TRUE.${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='FALSE'
xlab='NULL'
ylab='NULL'
xvariable='xvariable'
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=''
vline=0
facet=''
facet_o=''
xtics_pos=0
xtics_value=0
while getopts "hf:m:a:A:b:I:t:x:l:F:G:P:L:y:V: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=$OPTARG
;;
V)
vline=$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 ${y_add} -ne 0; then
scaleY="TRUE"
fi
mid='.lines_lm'
if test "${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")
}
data <- read.table(file="${file}", sep="\t", header=$header,
check.names=F, quote="")
pdf(file="${file}${mid}.pdf", onefile=FALSE,
paper="special", width=8, height=6, bg="white", pointsize=12)
plot(data, xlim=c(-100, 0), ylim=c(0, 100000), type='b',
xlab="Expression values",
ylab="Number of features", xaxt="n")
axis(1, at=seq(-100, 0, by=10),
labels=paste('>',seq(100,0,by=-10)))
filt_data <- data[data[,1] > -100 & data[,1] < -10, ]
fit <- lm(filt_data[,2] ~ filt_data[,1])
abline(fit, col='green', lwd=3)
dev.off()
#if(! $melted){
#
# data_rownames <- rownames(data)
# data_colnames <- colnames(data)
# data\$${xvariable} <- data_rownames
# data_m <- melt(data, id.vars=c("${xvariable}"))
#} else {
# data_m <- read.table(file="$file", sep="\t",
# header=$header, check.names=F)
#}
#
#if (${y_add} != 0){
# data_m\$value <- data_m\$value + ${y_add}
#}
#
#if ("${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 (! ${x_type}){
# data_m\$${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=$xvariable, y=value, color=variable,
# group=variable)) +
# xlab("$xlab") + ylab("$ylab") + theme_bw() +
# theme(legend.title=element_blank(),
# panel.grid.major = element_blank(), panel.grid.minor = element_blank())
#
#p <- p ${facet}
#
#p <- p + expand_limits(y = 0)
##p <- p + scale_y_continuous(expand=c(0, 0))
#
#p <- p + theme(legend.key=element_blank())
#
##legend.background = element_rect(colour='white'))
#
##legend.background = element_rect(fill = "white"), legend.box=NULL,
##legend.margin=unit(0,"cm"))
#
#if (${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=${line_size})
# }else{
# p <- p + geom_line()
# }
#}
#
#if("$scaleY"){
# 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 (${xtics_angle} != 0){
# p <- p + theme(axis.text.x=element_text(angle=${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_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 <- ${vline}
#if(length(custom_vline_coord) > 1){
# p <- p + geom_vline(xintercept=custom_vline_coord,
# linetype="dotted" )
#}
#
#p <- p${par}
#
##png(filename="${file}${mid}.png", width=$uwid, height=$vhig,
##res=$res)
#
#ggsave(p, filename="${file}${mid}.${ext}", dpi=$res, width=$uwid,
#height=$vhig, units=c("cm"))
END
if [ "$execute" == "TRUE" ]; then
Rscript ${file}${mid}.r
convert -density 150 ${file}${mid}.pdf ${file}${mid}.png
if [ "$?" == "0" ]; then /bin/rm -f ${file}${mid}.r; fi
fi
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