下載dotPlotly至本地威根，上傳到服務(wù)器解壓
https://github.com/tpoorten/dotPlotly/archive/refs/heads/master.zip
$ unzip ../software/dotPlotly-master.zip
進(jìn)入R
which R
/share/home/off_wenhao/biosoft/R-4.2.3/bin/R
添加R鏡像源
options(BioC_mirror="https://mirrors.tuna.tsinghua.edu.cn/bioconductor/")
options("repos" = c(CRAN="http://mirrors.cloud.tencent.com/CRAN/"))
options(download.file.method = 'libcurl')
options(url.method='libcurl')
安裝需要的R包
install.packages(c("optparse", "ggplot2", "plotly"))
測試腳本
./mummerCoordsDotPlotly.R -h
Usage: ./mummerCoordsDotPlotly.R -i alignments.coords -o out [options]
Options:
-i INPUT, --input=INPUT
coords file from mummer program 'show.coords' [default NULL]
-o OUTPUT, --output=OUTPUT
output filename prefix [default out]
-v, --verbose
Print out all parameter settings [default]
-q MIN-QUERY-LENGTH, --min-query-length=MIN-QUERY-LENGTH
filter queries with total alignments less than cutoff X bp [default 4e+05]
-m MIN-ALIGNMENT-LENGTH, --min-alignment-length=MIN-ALIGNMENT-LENGTH
filter alignments less than cutoff X bp [default 10000]
-p PLOT-SIZE, --plot-size=PLOT-SIZE
plot size X by X inches [default 15]
-l, --show-horizontal-lines
turn on horizontal lines on plot for separating scaffolds [default FALSE]
-k NUMBER-REF-CHROMOSOMES, --number-ref-chromosomes=NUMBER-REF-CHROMOSOMES
number of sorted reference chromosomes to keep [default all chromosmes]
-s, --identity
turn on color alignments by % identity [default FALSE]
-t, --identity-on-target
turn on calculation of % identity for on-target alignments only [default FALSE]
-x, --interactive-plot-off
turn off production of interactive plotly [default TRUE]
-r REFERENCE-IDS, --reference-ids=REFERENCE-IDS
comma-separated list of reference IDs to keep [default NULL]
-h, --help
Show this help message and exit
$ ./pafCoordsDotPlotly.R -h
Usage: ./pafCoordsDotPlotly.R -i alignments.coords -o out [options]
Options:
-i INPUT, --input=INPUT
coords file from mummer program 'show.coords' [default NULL]
-o OUTPUT, --output=OUTPUT
output filename prefix [default out]
-v, --verbose
Print out all parameter settings [default]
-q MIN-QUERY-LENGTH, --min-query-length=MIN-QUERY-LENGTH
filter queries with total alignments less than cutoff X bp [default 4e+05]
-m MIN-ALIGNMENT-LENGTH, --min-alignment-length=MIN-ALIGNMENT-LENGTH
filter alignments less than cutoff X bp [default 10000]
-p PLOT-SIZE, --plot-size=PLOT-SIZE
plot size X by X inches [default 15]
-l, --show-horizontal-lines
turn on horizontal lines on plot for separating scaffolds [default FALSE]
-k NUMBER-REF-CHROMOSOMES, --number-ref-chromosomes=NUMBER-REF-CHROMOSOMES
number of sorted reference chromosomes to keep [default all chromosmes]
-s, --identity
turn on color alignments by % identity [default FALSE]
-t, --identity-on-target
turn on calculation of % identity for on-target alignments only [default FALSE]
-x, --interactive-plot-off
turn off production of interactive plotly [default TRUE]
-r REFERENCE-IDS, --reference-ids=REFERENCE-IDS
comma-separated list of reference IDs to keep [default NULL]
-h, --help
Show this help message and exit
數(shù)據(jù)測試
nucmer -t 20 --mum --mincluster 500 --prefix=OUT PAH.chrom.fa groups.chrom.fa > OUT.delta
delta-filter -1 -i 90 -l 10000 -q OUT.delta > OUT.filter1.delta
show-coords -c -r OUT.filter1.delta > OUT.filter1.coords
#mummerplot -p 10k --large --png OUT.filter1.delta
mummerCoordsDotPlotly.R -i OUT.filter1.coords -o out -s -t -m 500 -q 500000 -k 7 -l
注意：
.coords格式用mummerCoordsDotPlotly.R腳本
show-coords -c example.delta > example.coords
mummerCoordsDotPlotly.R -i example.coords -o out -s -t -m 500 -q 500000 -k 7 -l
.paf格式用pafCoordsDotPlotly.R腳本
pafCoordsDotPlotly.R -i example.paf -o out -s -t -m 500 -q 500000 -k 7 -l
