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recos's Introduction

recos(plot genomic characteristics and collinearity)

1. Quick start

install

step1: Install Singularity in your OS, you can refer https://docs.sylabs.io/guides/latest/user-guide/quick_start.html.

step2: git clone https://github.com/zhk2017/recos.git, cd recos/exe && chmod 755 recos

step3: download base img: https://pan.baidu.com/s/1e54jrCk62SSvFcr8o7tMoA , Extraction code: q2e5

step4: base img file name is recos.sif, wo should mv base img recos.sif in img directory(cloned directory).

如果基础镜像链接失效,或者有其他问题,请加我微信,微信号:wxid_h7ip07mfu4l312

2. Example dataset

There are five example dataset for beginers, change the directory into the tutorials data path, and sh run.sh. when the job is finished, a SVG format picture will be generated. You can use Chromo browser to open it.

perl recos_wrapper.pl -c example.ini -o example

-c configure file for plot

-o output fileanme, auto add .svg suffix

3. Cofingure file

    [canvas]   #用于定义整个画布的大小、图形方向、图形元素所在的位置和大小等
    width  = 2000  #画布宽度,像素
    height = 1200  #画布高度,像素
    direction = vertical  #图形元素的方向,水平或垂直
    axis_ratio = 0.05  #坐标轴占画布的大小,0.05表示占总大小的5%,举例:如果direction为水平,表示占高度的5%
    name_ratio = 0.05  #染色体名称占画布的大小
    margin = 10,10,10,10  #画布四周留白的大小,像素
    inner_ratio = 0.15,0.2,0.3,0.2,0.15 #每个染色体对占一个区域,里面分为5部分,详见后面对参数的说明
    
    [axis]
    canvas_position = left  #坐标轴在画布中的位置,举例:如果direction为水平,则只能是上或下
    ticks_minor = 1Mb  #坐标轴中较短刻度的步长
    ticks_major = 5Mb  #坐标轴较长刻度的步长
    ticks_minor_len = -5  #较短刻度的长度,像素,负值可以调整方向
    ticks_major_len = -10 #较长刻度的长度,像素,负值可以调整方向
    axis_line = 0.7  #以坐标轴区域为参考,坐标轴主线在里面的位置,举例:0.5表示居中
    axis_color = rgb(0,0,0)  #坐标轴颜色
    axis_label = 0.2  #以坐标轴区域为参考,刻度标签名称所在位置
    axis_label_size = 12  #刻度标签名称的大小,像素
    axis_label_color = rgb(0,255,255)  #刻度标签名称的颜色
    axis_width = 1  #坐标轴线条宽度
    axis_opacity = 1 #坐标轴线条透明度
    label_unit = Mb  #刻度标签名称的单位
    
    [chromosome]
    canvas_position = bottom  #展示染色体比较的绘图元素在画布中的位置
    chromosome_list = /data/example/ref_query.list  #定义染色体比较关系、条带颜色、染色体长度、透明度、比较ID等
    chroms = 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20 #比较ID的列表在chromosome_list定义,指定展示顺序
    name_position = center  #染色体名称标签的位置
    round=15 #设置染色体条带两端为圆形,单位像素,越大弧度越大,默认为0,表示直角
    
    >[ref_out1]  #定义参考基因组外侧要展示的图形元素
    file =/data/PAV/ref.bed
    type = hist  #以直方图展示
    pos0 = 0  #起始位置,最小为0
    pos1 = 1  #终止位置,最大为1,可以是小数
    low_color = rgb(0,0,0) #低位色
    color = rgb(0, 0, 255)  #颜色
    high_color =rgb(0, 0, 255) #高位色
    min = 100  #绘图时的最小值
    max = 5000  ##绘图时的最大值
    
    [ref_in1]  #定义参考基因组条带内部要展示的图形元素
    file = /data/example/gly.gc.bed
    type = heatmap  #以热图展示
    pos0 = 0
    pos1 = 1
    low_color = rgb(255,255,255)
    color = rgb(0, 0, 255)
    high_color =rgb(255, 0, 0)
    min = 0.3
    max = 0.5
    
    [qry_in1] #定义查询基因组条带内部要展示的图形元素
    file =/data/PAV/query.bed
    type = hist
    pos0 = 0
    pos1 = 1
    low_color = rgb(0,0,0)
    color = rgb(255, 0, 0)
    high_color =rgb(255, 0, 0)
    min = 100
    max = 5000
    
    [link1]  #定义染色体对的共线性关系,文件内部可以设置共线性块的颜色,来区分是否时SV,以????????
    coord = /data/coords.txt

4. Figure

example1 cd tutorials/example1 && sh run.sh

plot1

example2 cd tutorials/example2 && sh run.sh plot2

example3 cd tutorials/example3 && sh run.sh plot3

example4 cd tutorials/example4 && sh run.sh plot4

example5 cd tutorials/example5 && sh run.sh plot5

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