dotPlotly软件的安装及使用

下载dotPlotly至本地，上传到服务器解压

https://github.com/tpoorten/dotPlotly/archive/refs/heads/master.zip 

$ unzip ../software/dotPlotly-master.zip

进入R

which R
/share/home/off_wenhao/biosoft/R-4.2.3/bin/R

添加R镜像源

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')

安装需要的R包

install.packages(c("optparse", "ggplot2", "plotly"))

测试脚本

./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

数据测试

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脚本
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脚本
pafCoordsDotPlotly.R -i example.paf -o out -s -t -m 500 -q 500000 -k 7 -l