-
Notifications
You must be signed in to change notification settings - Fork 7
/
gwastoolkit.plotter.sh
executable file
·203 lines (183 loc) · 12.5 KB
/
gwastoolkit.plotter.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
#!/bin/bash
### Creating display functions
### Setting colouring
NONE='\033[00m'
OPAQUE='\033[2m'
FLASHING='\033[5m'
BOLD='\033[1m'
ITALIC='\033[3m'
UNDERLINE='\033[4m'
STRIKETHROUGH='\033[9m'
RED='\033[01;31m'
GREEN='\033[01;32m'
YELLOW='\033[01;33m'
PURPLE='\033[01;35m'
CYAN='\033[01;36m'
WHITE='\033[01;37m'
function echobold { #'echobold' is the function name
echo -e "${BOLD}${1}${NONE}" # this is whatever the function needs to execute, note ${1} is the text for echo
}
function echoitalic {
echo -e "${ITALIC}${1}${NONE}"
}
function echonooption {
echo -e "${OPAQUE}${RED}${1}${NONE}"
}
function echoerrorflash {
echo -e "${RED}${BOLD}${FLASHING}${1}${NONE}"
}
function echoerror {
echo -e "${RED}${1}${NONE}"
}
# errors no option
function echoerrornooption {
echo -e "${YELLOW}${1}${NONE}"
}
function echoerrorflashnooption {
echo -e "${YELLOW}${BOLD}${FLASHING}${1}${NONE}"
}
### MESSAGE FUNCTIONS
script_copyright_message() {
echo ""
THISYEAR=$(date +'%Y')
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "+ The MIT License (MIT) +"
echo "+ Copyright (c) 2015-${THISYEAR} Sander W. van der Laan +"
echo "+ +"
echo "+ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and +"
echo "+ associated documentation files (the \"Software\"), to deal in the Software without restriction, +"
echo "+ including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, +"
echo "+ and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, +"
echo "+ subject to the following conditions: +"
echo "+ +"
echo "+ The above copyright notice and this permission notice shall be included in all copies or substantial +"
echo "+ portions of the Software. +"
echo "+ +"
echo "+ THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT +"
echo "+ NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +"
echo "+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES +"
echo "+ OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN +"
echo "+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +"
echo "+ +"
echo "+ Reference: http://opensource.org. +"
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
}
script_arguments_error() {
echoerror "$1" # ERROR MESSAGE
echoerror ""
echoerror "- Argument #1 is path_to the configuration file."
echoerror "- Argument #2 is the phenotype analysed."
echoerror ""
echoerror "An example command would be: gwastoolkit.plotter.qc.sh [arg1: path_to_configuration_file] [arg2: phenotype]"
echoerror ""
echoerror "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
# The wrong arguments are passed, so we'll exit the script now!
exit 1
}
echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold " GWASTOOLKIT PLOTTER"
echobold " plotting of SNPTEST analysis results"
echobold ""
echobold " Version : v1.1.7"
echobold ""
echobold " Last update: 2023-11-29"
echobold " Written by : Sander W. van der Laan (s.w.vanderlaan-2@umcutrecht.nl)."
echobold ""
echobold " Testers : - Saskia Haitjema (s.haitjema@umcutrecht.nl)"
echobold " - Aisha Gohar (a.gohar@umcutrecht.nl)"
echobold " - Jessica van Setten (j.vansetten@umcutrecht.nl)"
echobold ""
echobold " Description: Plotting of a SNPTEST analysis: making Manhattan, Z-P, and QQ plots."
echobold ""
echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
### LOADING CONFIGURATION FILE
source "$1" # Depends on arg1.
### REQUIRED | GENERALS
CONFIGURATIONFILE="$1" # Depends on arg1 -- but also on where it resides!!!
PHENOTYPE="$2" # Depends on arg2
### START of if-else statement for the number of command-line arguments passed ###
if [[ $# -lt 2 ]]; then
echo "Oh, computer says no! Number of arguments found "$#"."
script_arguments_error "You must supply at least [2] arguments when plotting *** GWASToolKit *** results!"
echo ""
script_copyright_message
else
echo "All arguments are passed. These are the settings:"
### SET INPUT-DATA
OUTPUT_DIR=${PROJECTDIR}/${PROJECTNAME}/snptest_results/${PHENOTYPE} # depends on arg1
echo "The output directory is...................: ${OUTPUT_DIR}"
echo "The phenotypes is.........................: ${PHENOTYPE}"
echo ""
# PLOT GWAS RESULTS
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo " PLOTTING SNPTEST ANALYSIS RESULTS"
echo ""
echo "Please be patient...this can take a long time depending on the number of files."
echo "We started at: "$(date)
echo ""
SCRIPTS=${GWASTOOLKITDIR}/SCRIPTS
echo ""
echo "Plotting reformatted UNFILTERED data. Processing the following dataset: "
# what is the basename of the file?
RESULTS=${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.txt.gz
echo "* debug * ${RESULTS}"
FILENAME=$(basename ${RESULTS} .txt.gz)
echo "The basename is: "${FILENAME}
echo ""
### COLUMN NAMES & NUMBERS
### 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
### ALTID RSID CHR BP OtherAlleleA CodedAlleleB AvgMaxPostCall Info all_AA all_AB all_BB TotalN MAC MAF CAF HWE P BETA SE
### QQ-plot including 95%CI and compute lambda [P]
echo "Making QQ-plot including 95%CI and compute lambda..."
zcat ${RESULTS} | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col P | tail -n +2 | grep -v NA > ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_CI.txt
# Rscript ${SCRIPTS}/plotter.qq.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_CI.txt -o ${OUTPUT_DIR} -s PVAL -f PDF
Rscript ${SCRIPTS}/plotter.qq.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_CI.txt -o ${OUTPUT_DIR} -s PVAL -f PNG
echo ""
### QQ-plot stratified by effect allele frequency [P, EAF]
echo "QQ-plot stratified by effect allele frequency..."
zcat ${RESULTS} | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col P,CAF | tail -n +2 | grep -v NA > ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_EAF.txt
# Rscript ${SCRIPTS}/plotter.qq_by_caf.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_EAF.txt -o ${OUTPUT_DIR} -s PVAL -f PDF
Rscript ${SCRIPTS}/plotter.qq_by_caf.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_EAF.txt -o ${OUTPUT_DIR} -s PVAL -f PNG
echo ""
## QQ-plot stratified by imputation quality (info -- imputation quality) [P, INFO]
echo "QQ-plot stratified by imputation quality..."
zcat ${RESULTS} | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col P,Info | tail -n +2 | grep -v NA > ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_INFO.txt
# Rscript ${SCRIPTS}/plotter.qq_by_info.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_INFO.txt -o ${OUTPUT_DIR} -s PVAL -f PDF
Rscript ${SCRIPTS}/plotter.qq_by_info.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_INFO.txt -o ${OUTPUT_DIR} -s PVAL -f PNG
echo ""
### Plot the imputation quality (info) in a histogram [INFO]
echo "Plot the imputation quality (info) in a histogram..."
zcat ${RESULTS} | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col Info | tail -n +2 | grep -v NA > ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Histogram_INFO.txt
# Rscript ${SCRIPTS}/plotter.infoscore.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Histogram_INFO.txt -o ${OUTPUT_DIR} -f PDF
Rscript ${SCRIPTS}/plotter.infoscore.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Histogram_INFO.txt -o ${OUTPUT_DIR} -f PNG
echo ""
### Plot the BETAs in a histogram [BETA]
echo "Plot the BETAs in a histogram..."
zcat ${RESULTS} | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col BETA | tail -n +2 | grep -v NA > ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Histogram_BETA.txt
# Rscript ${SCRIPTS}/plotter.effectsize.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Histogram_BETA.txt -o ${OUTPUT_DIR} -f PDF
Rscript ${SCRIPTS}/plotter.effectsize.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Histogram_BETA.txt -o ${OUTPUT_DIR} -f PNG
echo ""
### Plot the Z-score based p-value (calculated from beta/se) and P [BETA, SE, P]
echo "Plot the Z-score based p-value (calculated from beta/se) and P..."
zcat ${RESULTS} | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col BETA,SE,P | tail -n +2 | grep -v NA > ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.PZ_Plot.txt
# Rscript ${SCRIPTS}/plotter.p_z.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.PZ_Plot.txt -o ${OUTPUT_DIR} -s 500000 -f PDF
Rscript ${SCRIPTS}/plotter.p_z.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.PZ_Plot.txt -o ${OUTPUT_DIR} -s 500000 -f PNG
echo ""
### Manhattan plot for quick inspection (truncated upto -log10(p-value)) [CHR, BP, P]
echo "Manhattan plot for quick inspection (truncated upto -log10(p-value)=2)..."
zcat ${RESULTS} | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col CHR,BP,P | tail -n +2 | grep -v NA > ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Manhattan_forQuickInspect.txt
# Rscript ${SCRIPTS}/plotter.manhattan.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Manhattan_forQuickInspect.txt -o ${OUTPUT_DIR} -c QC -f PDF -t ${FILENAME}
Rscript ${SCRIPTS}/plotter.manhattan.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Manhattan_forQuickInspect.txt -o ${OUTPUT_DIR} -c QC -f PNG -t ${FILENAME}
echo ""
echo "Finished plotting, zipping up and re-organising intermediate files!"
rm -v ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_CI.txt
rm -v ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_EAF.txt
rm -v ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.QQplot_INFO.txt
rm -v ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Histogram_INFO.txt
rm -v ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Histogram_BETA.txt
rm -v ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.PZ_Plot.txt
rm -v ${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.Manhattan_forQuickInspect.txt
echo ""
### END of if-else statement for the number of command-line arguments passed ###
fi
# script_copyright_message