zoukankan      html  css  js  c++  java
  • 关于 GraPhlAn 的孤独自学

    最近需要用 GraPhlan 来绘制 taxo分类图稍微研究了一下

    一、简介

    官网: http://huttenhower.sph.harvard.edu/GraPhlAn

    主要有两个脚本:

      graphlan_annotate.py:将原始文件和注释文件合并的,作为 graphlan.py 的输入文件进行绘图

      graphlan.py:根据输入文件绘图

    Options 分为 4 类(详细选项可以见官网):

      Global tree options:树的枝长等选项

      Graphical tree options:树上的一些图形选项

      Annotation options:对树上物种的注释选项

      Ring options:树外环形图的注释选项

    二、学习方法的寻找

    我们服务器有该软件,所以无需安装。软件会有 examples 目录,入门级可参考 examples/guide 目录。于是我参考了该目录的内容。

    guide 目录中:all.sh

     1 source /software/graphlan/activate.sh
     2 ##原始
     3 graphlan.py guide.txt step_0.png --dpi 300 --size 3.5
     4 ##加入线条信息
     5 graphlan_annotate.py --annot annot_0.txt guide.txt guide_1.xml
     6 graphlan.py guide_1.xml step_1.png --dpi 300 --size 3.5
     7 ##加入图像信息
     8 graphlan_annotate.py --annot annot_1.txt guide_1.xml guide_2.xml
     9 graphlan.py guide_2.xml step_2.png --dpi 300 --size 3.5
    10 ##加入注释信息
    11 graphlan_annotate.py --annot annot_2.txt guide_2.xml guide_3.xml
    12 graphlan.py guide_3.xml step_3.png --dpi 300 --size 3.5
    13 ##加入外环信息
    14 graphlan_annotate.py --annot annot_3.txt guide_3.xml guide_4.xml
    15 graphlan.py guide_4.xml step_4.png --dpi 300 --size 3.5 --pad 0.0

    三、对于 all.sh 的解读 

    以上内容得到结果如下图:

     

    1. 第三行

    graphlan.py guide.txt step_0.png --dpi 300 --size 3.5

    输入文件各分类水平以 "."  为分隔,用该文件进行绘图,得到一张没有任何注释的分类树,见图 a。输入文件为 guide.txt:

    Bacillaceae.Anoxybacillus.Aflavithermus
    Bacillaceae.Bacillus.Bamyloliquefaciens
    Bacillaceae.Bacillus.Banthracis
    Bacillaceae.Bacillus.Batrophaeus
    Bacillaceae.Bacillus.Bcellulosilyticus
    Bacillaceae.Bacillus.Bcereus
    Bacillaceae.Bacillus.Bclausii
    Bacillaceae.Bacillus.Bcoagulans
    Bacillaceae.Bacillus.Bcoahuilensis
    Bacillaceae.Bacillus.Bhalodurans
    Bacillaceae.Bacillus.Blicheniformis
    Bacillaceae.Bacillus.Bmegaterium
    Bacillaceae.Bacillus.Bmycoides
    Bacillaceae.Bacillus.Bpseudofirmus
    Bacillaceae.Bacillus.Bpseudomycoides
    Bacillaceae.Bacillus.Bpumilus
    Bacillaceae.Bacillus.Bselenitireducens
    Bacillaceae.Bacillus.Bsubtilis
    Bacillaceae.Bacillus.Bthuringiensis
    Bacillaceae.Bacillus.Bweihenstephanensis
    Bacillaceae.Caldalkalibacillus.Cthermarum
    Bacillaceae.Geobacillus.Gkaustophilus
    Bacillaceae.Geobacillus.Gthermodenitrificans
    Bacillaceae.Geobacillus.Gthermoglucosidasius
    Bacillaceae.Lysinibacillus.Lfusiformis
    Bacillaceae.Lysinibacillus.Lsphaericus
    Bacillaceae.Oceanobacillus.Oiheyensis
    Listeriaceae.Listeria.Lgrayi
    Listeriaceae.Listeria.Linnocua
    Listeriaceae.Listeria.Lmonocytogenes
    Listeriaceae.Listeria.Lseeligeri
    Listeriaceae.Listeria.Lwelshimeri
    Paenibacillaceae.Brevibacillus.Bbrevis
    Paenibacillaceae.Brevibacillus.Blaterosporus
    Paenibacillaceae.Paenibacillus.Pcurdlanolyticus
    Paenibacillaceae.Paenibacillus.Plarvae
    Paenibacillaceae.Paenibacillus.Pmucilaginosus
    Paenibacillaceae.Paenibacillus.Ppolymyxa
    Paenibacillaceae.Paenibacillus.Pvortex
    Staphylococcaceae.Macrococcus.Mcaseolyticus
    Staphylococcaceae.Staphylococcus.Saureus
    Staphylococcaceae.Staphylococcus.Scapitis
    Staphylococcaceae.Staphylococcus.Scaprae
    Staphylococcaceae.Staphylococcus.Scarnosus
    Staphylococcaceae.Staphylococcus.Sepidermidis
    Staphylococcaceae.Staphylococcus.Shaemolyticus
    Staphylococcaceae.Staphylococcus.Shominis
    Staphylococcaceae.Staphylococcus.Slugdunensis
    Staphylococcaceae.Staphylococcus.Spseudintermedius
    Staphylococcaceae.Staphylococcus.Ssaprophyticus
    Staphylococcaceae.Staphylococcus.Swarneri
    guide.txt

    2. 第五、六行

    graphlan_annotate.py --annot annot_0.txt guide.txt guide_1.xml
    graphlan.py guide_1.xml step_1.png --dpi 300 --size 3.5
    

     在原始输入文件的基础上,加入 annot_0.txt ,然后进行绘图,得到了树图的注释,见图 b。该文件使用了 Global tree options,来设置树图的枝长、粗细等。

    clade_separation        0.5
    branch_thickness        1.5
    branch_bracket_depth    0.8
    branch_bracket_width    0.25
    clade_marker_size       80
    clade_marker_edge_color #555555
    clade_marker_edge_width 1.2
    annot_0.txt

    3. 第八、九行

    graphlan_annotate.py --annot annot_1.txt guide_1.xml guide_2.xml
    graphlan.py guide_2.xml step_2.png --dpi 300 --size 3.5
    

     在以上的基础上,加入 annot_1.txt,然后进行绘图,得到图 c。该文件使用了 Graphical tree options,来设置树图中,枝的颜色、点的图形颜色等。

    Proteobacteria      clade_marker_color      b
    Proteobacteria      clade_marker_size       80
    Candidatus_Moranbacteria clade_marker_color      r
    Candidatus_Moranbacteria clade_marker_size       125
    Acidobacteria        clade_marker_color      b
    Acidobacteria        clade_marker_size       120
    Acidobacteria        clade_marker_shape      h
    Chloroflexi        clade_marker_color      #20DD20
    Plarvae clade_marker_color      #008000
    Pmucilaginosus  clade_marker_color      #057005
    Ppolymyxa       clade_marker_color      #009020
    Pvortex clade_marker_color      #00AA00
    Bacillaceae     clade_marker_shape      *
    Bacillaceae     clade_marker_size       130
    Bacillaceae     clade_marker_color      b
    Bacteria    clade_marker_shape      *
    Bacteria    clade_marker_size       130
    Paenibacillaceae        clade_marker_shape      *
    Paenibacillaceae        clade_marker_size       130
    Paenibacillaceae        clade_marker_color      g
    Staphylococcaceae       clade_marker_shape      *
    Staphylococcaceae       clade_marker_size       130
    Staphylococcaceae       clade_marker_color      r
    Batrophaeus     clade_marker_size       12
    Bcellulosilyticus       clade_marker_size       8
    Bcereus clade_marker_size       3
    Scarnosus       clade_marker_size       75
    Plarvae clade_marker_size       89
    Bpumilus        clade_marker_size       50
    Bsubtilis       clade_marker_size       65
    Bthuringiensis  clade_marker_size       10
    Cthermarum      clade_marker_size       15
    Bmegaterium     clade_marker_size       12
    Lfusiformis     clade_marker_size       174
    Oiheyensis      clade_marker_size       95
    Scapitis        clade_marker_size       36
    Shaemolyticus   clade_marker_size       64
    Ppolymyxa       clade_marker_size       20
    Pvortex clade_marker_size       19
    Swarneri        clade_marker_size       33
    Spseudintermedius       clade_marker_size       19
    annot_1.txt

    4. 第十一、十二行

    graphlan_annotate.py --annot annot_2.txt guide_2.xml guide_3.xml
    graphlan.py guide_3.xml step_3.png --dpi 300 --size 3.5
    

     在以上的基础上,加入 annot_2.txt,然后进行绘图,得到图 d。该文件使用了 Annotation options,来设置树图的注释信息。

    Proteobacteria      clade_marker_color      b
    Proteobacteria      clade_marker_size       80
    Candidatus_Moranbacteria clade_marker_color      r
    Candidatus_Moranbacteria clade_marker_size       125
    Acidobacteria        clade_marker_color      b
    Acidobacteria        clade_marker_size       120
    Acidobacteria        clade_marker_shape      h
    Chloroflexi        clade_marker_color      #20DD20
    Plarvae clade_marker_color      #008000
    Pmucilaginosus  clade_marker_color      #057005
    Ppolymyxa       clade_marker_color      #009020
    Pvortex clade_marker_color      #00AA00
    Bacillaceae     clade_marker_shape      *
    Bacillaceae     clade_marker_size       130
    Bacillaceae     clade_marker_color      b
    Bacteria    clade_marker_shape      *
    Bacteria    clade_marker_size       130
    Paenibacillaceae        clade_marker_shape      *
    Paenibacillaceae        clade_marker_size       130
    Paenibacillaceae        clade_marker_color      g
    Staphylococcaceae       clade_marker_shape      *
    Staphylococcaceae       clade_marker_size       130
    Staphylococcaceae       clade_marker_color      r
    Batrophaeus     clade_marker_size       12
    Bcellulosilyticus       clade_marker_size       8
    Bcereus clade_marker_size       3
    Scarnosus       clade_marker_size       75
    Plarvae clade_marker_size       89
    Bpumilus        clade_marker_size       50
    Bsubtilis       clade_marker_size       65
    Bthuringiensis  clade_marker_size       10
    Cthermarum      clade_marker_size       15
    Bmegaterium     clade_marker_size       12
    Lfusiformis     clade_marker_size       174
    Oiheyensis      clade_marker_size       95
    Scapitis        clade_marker_size       36
    Shaemolyticus   clade_marker_size       64
    Ppolymyxa       clade_marker_size       20
    Pvortex clade_marker_size       19
    Swarneri        clade_marker_size       33
    Spseudintermedius       clade_marker_size       19
    annot_2.txt

    5. 第十四、十五行

    graphlan_annotate.py --annot annot_3.txt guide_3.xml guide_4.xml
    graphlan.py guide_4.xml step_4.png --dpi 300 --size 3.5 --pad 0.0
    

     在以上的技术上,加入 annot_3.txt,然后进行绘图,得到图 e。该文件使用了 Ring options,来绘制树外的环形图。

    ring_internal_separator_thickness    1    0.5
    ring_internal_separator_thickness    2    1.0
    ring_internal_separator_thickness    3    0.5
    ring_internal_separator_thickness    4    0.5
    ring_internal_separator_thickness    5    1.0
    ring_width    1    0.5
    ring_height    1    0.75
    ring_width    5    0.5
    Bacillaceae.Anoxybacillus.Aflavithermus    ring_shape    1    v
    Bacillaceae.Bacillus.Bamyloliquefaciens    ring_shape    1    v
    Bacillaceae.Bacillus.Banthracis    ring_shape    1    ^
    Bacillaceae.Bacillus.Batrophaeus    ring_shape    1    v
    Bacillaceae.Bacillus.Bcellulosilyticus    ring_shape    1    ^
    Bacillaceae.Bacillus.Bcereus    ring_shape    1    ^
    Bacillaceae.Bacillus.Bclausii    ring_shape    1    ^
    Bacillaceae.Bacillus.Bcoagulans    ring_shape    1    v
    Bacillaceae.Bacillus.Bcoahuilensis    ring_shape    1    ^
    Bacillaceae.Bacillus.Bhalodurans    ring_shape    1    v
    Bacillaceae.Bacillus.Blicheniformis    ring_shape    1    ^
    Bacillaceae.Bacillus.Bmegaterium    ring_shape    1    v
    Bacillaceae.Bacillus.Bmycoides    ring_shape    1    v
    Bacillaceae.Bacillus.Bpseudofirmus    ring_shape    1    ^
    Bacillaceae.Bacillus.Bpseudomycoides    ring_shape    1    v
    Bacillaceae.Bacillus.Bpumilus    ring_shape    1    v
    Bacillaceae.Bacillus.Bselenitireducens    ring_shape    1    ^
    Bacillaceae.Bacillus.Bsubtilis    ring_shape    1    v
    Bacillaceae.Bacillus.Bthuringiensis    ring_shape    1    ^
    Bacillaceae.Bacillus.Bweihenstephanensis    ring_shape    1    ^
    Bacillaceae.Caldalkalibacillus.Cthermarum    ring_shape    1    ^
    Bacillaceae.Geobacillus.Gkaustophilus    ring_shape    1    v
    Bacillaceae.Geobacillus.Gthermodenitrificans    ring_shape    1    ^
    Bacillaceae.Geobacillus.Gthermoglucosidasius    ring_shape    1    v
    Bacillaceae.Lysinibacillus.Lfusiformis    ring_shape    1    v
    Bacillaceae.Lysinibacillus.Lsphaericus    ring_shape    1    ^
    Bacillaceae.Oceanobacillus.Oiheyensis    ring_shape    1    v
    Listeriaceae.Listeria.Lgrayi    ring_shape    1    v
    Listeriaceae.Listeria.Linnocua    ring_shape    1    ^
    Listeriaceae.Listeria.Lmonocytogenes    ring_shape    1    ^
    Listeriaceae.Listeria.Lseeligeri    ring_shape    1    v
    Listeriaceae.Listeria.Lwelshimeri    ring_shape    1    ^
    Paenibacillaceae.Brevibacillus.Bbrevis    ring_shape    1    v
    Paenibacillaceae.Brevibacillus.Blaterosporus    ring_shape    1    ^
    Paenibacillaceae.Paenibacillus.Pcurdlanolyticus    ring_shape    1    v
    Paenibacillaceae.Paenibacillus.Plarvae    ring_shape    1    v
    Paenibacillaceae.Paenibacillus.Pmucilaginosus    ring_shape    1    v
    Paenibacillaceae.Paenibacillus.Ppolymyxa    ring_shape    1    v
    Paenibacillaceae.Paenibacillus.Pvortex    ring_shape    1    ^
    Staphylococcaceae.Macrococcus.Mcaseolyticus    ring_shape    1    ^
    Staphylococcaceae.Staphylococcus.Saureus    ring_shape    1    ^
    Staphylococcaceae.Staphylococcus.Scapitis    ring_shape    1    ^
    Staphylococcaceae.Staphylococcus.Scaprae    ring_shape    1    v
    Staphylococcaceae.Staphylococcus.Scarnosus    ring_shape    1    v
    Staphylococcaceae.Staphylococcus.Sepidermidis    ring_shape    1    v
    Staphylococcaceae.Staphylococcus.Shaemolyticus    ring_shape    1    ^
    Staphylococcaceae.Staphylococcus.Shominis    ring_shape    1    ^
    Staphylococcaceae.Staphylococcus.Slugdunensis    ring_shape    1    v
    Staphylococcaceae.Staphylococcus.Spseudintermedius    ring_shape    1    ^
    Staphylococcaceae.Staphylococcus.Ssaprophyticus    ring_shape    1    v
    Staphylococcaceae.Staphylococcus.Swarneri    ring_shape    1    ^
    Bacillaceae.Anoxybacillus.Aflavithermus    ring_alpha    2    0.423462136478
    Bacillaceae.Bacillus.Bamyloliquefaciens    ring_alpha    2    0.328914114867
    Bacillaceae.Bacillus.Banthracis    ring_alpha    2    0.699584495953
    Bacillaceae.Bacillus.Batrophaeus    ring_alpha    2    0.914291471541
    Bacillaceae.Bacillus.Bcellulosilyticus    ring_alpha    2    0.777833777684
    Bacillaceae.Bacillus.Bcereus    ring_alpha    2    0.594773291359
    Bacillaceae.Bacillus.Bclausii    ring_alpha    2    0.444201154337
    Bacillaceae.Bacillus.Bcoagulans    ring_alpha    2    0.85140222384
    Bacillaceae.Bacillus.Bcoahuilensis    ring_alpha    2    0.445070000889
    Bacillaceae.Bacillus.Bhalodurans    ring_alpha    2    0.436455399115
    Bacillaceae.Bacillus.Blicheniformis    ring_alpha    2    0.570138625829
    Bacillaceae.Bacillus.Bmegaterium    ring_alpha    2    0.331044708077
    Bacillaceae.Bacillus.Bmycoides    ring_alpha    2    0.134087953967
    Bacillaceae.Bacillus.Bpseudofirmus    ring_alpha    2    0.959809786409
    Bacillaceae.Bacillus.Bpseudomycoides    ring_alpha    2    0.322425841569
    Bacillaceae.Bacillus.Bpumilus    ring_alpha    2    0.6310797781
    Bacillaceae.Bacillus.Bselenitireducens    ring_alpha    2    0.0999247790029
    Bacillaceae.Bacillus.Bsubtilis    ring_alpha    2    0.0291140916975
    Bacillaceae.Bacillus.Bthuringiensis    ring_alpha    2    0.291201092034
    Bacillaceae.Bacillus.Bweihenstephanensis    ring_alpha    2    0.298583691605
    Bacillaceae.Caldalkalibacillus.Cthermarum    ring_alpha    2    0.0534558636274
    Bacillaceae.Geobacillus.Gkaustophilus    ring_alpha    2    0.0878700889869
    Bacillaceae.Geobacillus.Gthermodenitrificans    ring_alpha    2    0.914114387261
    Bacillaceae.Geobacillus.Gthermoglucosidasius    ring_alpha    2    0.161880353101
    Bacillaceae.Lysinibacillus.Lfusiformis    ring_alpha    2    0.730306130149
    Bacillaceae.Lysinibacillus.Lsphaericus    ring_alpha    2    0.334890327634
    Bacillaceae.Oceanobacillus.Oiheyensis    ring_alpha    2    0.218075337012
    Listeriaceae.Listeria.Lgrayi    ring_alpha    2    0.447942203556
    Listeriaceae.Listeria.Linnocua    ring_alpha    2    0.143522097769
    Listeriaceae.Listeria.Lmonocytogenes    ring_alpha    2    0.324901346814
    Listeriaceae.Listeria.Lseeligeri    ring_alpha    2    0.721461557745
    Listeriaceae.Listeria.Lwelshimeri    ring_alpha    2    0.603871257827
    Paenibacillaceae.Brevibacillus.Bbrevis    ring_alpha    2    0.536829482998
    Paenibacillaceae.Brevibacillus.Blaterosporus    ring_alpha    2    0.75932144025
    Paenibacillaceae.Paenibacillus.Pcurdlanolyticus    ring_alpha    2    0.904283082241
    Paenibacillaceae.Paenibacillus.Plarvae    ring_alpha    2    0.253696705619
    Paenibacillaceae.Paenibacillus.Pmucilaginosus    ring_alpha    2    0.820910759872
    Paenibacillaceae.Paenibacillus.Ppolymyxa    ring_alpha    2    0.783643352935
    Paenibacillaceae.Paenibacillus.Pvortex    ring_alpha    2    0.781101978268
    Staphylococcaceae.Macrococcus.Mcaseolyticus    ring_alpha    2    0.597634927522
    Staphylococcaceae.Staphylococcus.Saureus    ring_alpha    2    0.639595480173
    Staphylococcaceae.Staphylococcus.Scapitis    ring_alpha    2    0.326481586152
    Staphylococcaceae.Staphylococcus.Scaprae    ring_alpha    2    0.48661102115
    Staphylococcaceae.Staphylococcus.Scarnosus    ring_alpha    2    0.757163548806
    Staphylococcaceae.Staphylococcus.Sepidermidis    ring_alpha    2    0.899268566505
    Staphylococcaceae.Staphylococcus.Shaemolyticus    ring_alpha    2    0.895335711479
    Staphylococcaceae.Staphylococcus.Shominis    ring_alpha    2    0.272427614396
    Staphylococcaceae.Staphylococcus.Slugdunensis    ring_alpha    2    0.710528488721
    Staphylococcaceae.Staphylococcus.Spseudintermedius    ring_alpha    2    0.24185085998
    Staphylococcaceae.Staphylococcus.Ssaprophyticus    ring_alpha    2    0.0895481129751
    Staphylococcaceae.Staphylococcus.Swarneri    ring_alpha    2    0.00539683704551
    Bacillaceae.Anoxybacillus.Aflavithermus    ring_color    2    #AAAA00
    Bacillaceae.Bacillus.Bamyloliquefaciens    ring_color    2    #AAAA00
    Bacillaceae.Bacillus.Banthracis    ring_color    2    #AAAA00
    Bacillaceae.Bacillus.Batrophaeus    ring_color    2    #AAAA00
    Bacillaceae.Bacillus.Bcellulosilyticus    ring_color    2    #AAAA00
    Bacillaceae.Bacillus.Bcereus    ring_color    2    #AAAA00
    Bacillaceae.Bacillus.Bclausii    ring_color    2    #AAAA00
    Bacillaceae.Bacillus.Bcoagulans    ring_color    2    #AAAA00
    Bacillaceae.Bacillus.Bcoahuilensis    ring_color    2    #AAAA00
    Bacillaceae.Bacillus.Bhalodurans    ring_color    2    #AAAA00
    Bacillaceae.Bacillus.Blicheniformis    ring_color    2    #AAAA00
    Bacillaceae.Bacillus.Bmegaterium    ring_color    2    #AAAA00
    Bacillaceae.Bacillus.Bmycoides    ring_color    2    #AAAA00
    Bacillaceae.Bacillus.Bpseudofirmus    ring_color    2    #AAAA00
    Bacillaceae.Bacillus.Bpseudomycoides    ring_color    2    #AAAA00
    Bacillaceae.Bacillus.Bpumilus    ring_color    2    #AAAA00
    Bacillaceae.Bacillus.Bselenitireducens    ring_color    2    #AAAA00
    Bacillaceae.Bacillus.Bsubtilis    ring_color    2    #AAAA00
    Bacillaceae.Bacillus.Bthuringiensis    ring_color    2    #AAAA00
    Bacillaceae.Bacillus.Bweihenstephanensis    ring_color    2    #AAAA00
    Bacillaceae.Caldalkalibacillus.Cthermarum    ring_color    2    #AAAA00
    Bacillaceae.Geobacillus.Gkaustophilus    ring_color    2    #AAAA00
    Bacillaceae.Geobacillus.Gthermodenitrificans    ring_color    2    #AAAA00
    Bacillaceae.Geobacillus.Gthermoglucosidasius    ring_color    2    #AAAA00
    Bacillaceae.Lysinibacillus.Lfusiformis    ring_color    2    #AAAA00
    Bacillaceae.Lysinibacillus.Lsphaericus    ring_color    2    #AAAA00
    Bacillaceae.Oceanobacillus.Oiheyensis    ring_color    2    #AAAA00
    Listeriaceae.Listeria.Lgrayi    ring_color    2    #AAAA00
    Listeriaceae.Listeria.Linnocua    ring_color    2    #AAAA00
    Listeriaceae.Listeria.Lmonocytogenes    ring_color    2    #AAAA00
    Listeriaceae.Listeria.Lseeligeri    ring_color    2    #AAAA00
    Listeriaceae.Listeria.Lwelshimeri    ring_color    2    #AAAA00
    Paenibacillaceae.Brevibacillus.Bbrevis    ring_color    2    #AAAA00
    Paenibacillaceae.Brevibacillus.Blaterosporus    ring_color    2    #AAAA00
    Paenibacillaceae.Paenibacillus.Pcurdlanolyticus    ring_color    2    #AAAA00
    Paenibacillaceae.Paenibacillus.Plarvae    ring_color    2    #AAAA00
    Paenibacillaceae.Paenibacillus.Pmucilaginosus    ring_color    2    #AAAA00
    Paenibacillaceae.Paenibacillus.Ppolymyxa    ring_color    2    #AAAA00
    Paenibacillaceae.Paenibacillus.Pvortex    ring_color    2    #AAAA00
    Staphylococcaceae.Macrococcus.Mcaseolyticus    ring_color    2    #AAAA00
    Staphylococcaceae.Staphylococcus.Saureus    ring_color    2    #AAAA00
    Staphylococcaceae.Staphylococcus.Scapitis    ring_color    2    #AAAA00
    Staphylococcaceae.Staphylococcus.Scaprae    ring_color    2    #AAAA00
    Staphylococcaceae.Staphylococcus.Scarnosus    ring_color    2    #AAAA00
    Staphylococcaceae.Staphylococcus.Sepidermidis    ring_color    2    #AAAA00
    Staphylococcaceae.Staphylococcus.Shaemolyticus    ring_color    2    #AAAA00
    Staphylococcaceae.Staphylococcus.Shominis    ring_color    2    #AAAA00
    Staphylococcaceae.Staphylococcus.Slugdunensis    ring_color    2    #AAAA00
    Staphylococcaceae.Staphylococcus.Spseudintermedius    ring_color    2    #AAAA00
    Staphylococcaceae.Staphylococcus.Ssaprophyticus    ring_color    2    #AAAA00
    Staphylococcaceae.Staphylococcus.Swarneri    ring_color    2    #AAAA00
    Bacillaceae.Anoxybacillus.Aflavithermus    ring_alpha    3    0.486328798075
    Bacillaceae.Bacillus.Bamyloliquefaciens    ring_alpha    3    0.902536860011
    Bacillaceae.Bacillus.Banthracis    ring_alpha    3    0.540967223446
    Bacillaceae.Bacillus.Batrophaeus    ring_alpha    3    0.514745187899
    Bacillaceae.Bacillus.Bcellulosilyticus    ring_alpha    3    0.808744341053
    Bacillaceae.Bacillus.Bcereus    ring_alpha    3    0.174551783411
    Bacillaceae.Bacillus.Bclausii    ring_alpha    3    0.355096857237
    Bacillaceae.Bacillus.Bcoagulans    ring_alpha    3    0.30812498305
    Bacillaceae.Bacillus.Bcoahuilensis    ring_alpha    3    0.899878301907
    Bacillaceae.Bacillus.Bhalodurans    ring_alpha    3    0.135096627341
    Bacillaceae.Bacillus.Blicheniformis    ring_alpha    3    0.114946401925
    Bacillaceae.Bacillus.Bmegaterium    ring_alpha    3    0.112857448
    Bacillaceae.Bacillus.Bmycoides    ring_alpha    3    0.216895687759
    Bacillaceae.Bacillus.Bpseudofirmus    ring_alpha    3    0.728546119267
    Bacillaceae.Bacillus.Bpseudomycoides    ring_alpha    3    0.862047963812
    Bacillaceae.Bacillus.Bpumilus    ring_alpha    3    0.285139149368
    Bacillaceae.Bacillus.Bselenitireducens    ring_alpha    3    0.809501074306
    Bacillaceae.Bacillus.Bsubtilis    ring_alpha    3    0.261975858288
    Bacillaceae.Bacillus.Bthuringiensis    ring_alpha    3    0.887622203873
    Bacillaceae.Bacillus.Bweihenstephanensis    ring_alpha    3    0.964470847643
    Bacillaceae.Caldalkalibacillus.Cthermarum    ring_alpha    3    0.00503110917306
    Bacillaceae.Geobacillus.Gkaustophilus    ring_alpha    3    0.255498806201
    Bacillaceae.Geobacillus.Gthermodenitrificans    ring_alpha    3    0.617424889313
    Bacillaceae.Geobacillus.Gthermoglucosidasius    ring_alpha    3    0.378606726256
    Bacillaceae.Lysinibacillus.Lfusiformis    ring_alpha    3    0.997919879844
    Bacillaceae.Lysinibacillus.Lsphaericus    ring_alpha    3    0.707008809187
    Bacillaceae.Oceanobacillus.Oiheyensis    ring_alpha    3    0.479214513601
    Listeriaceae.Listeria.Lgrayi    ring_alpha    3    0.204916577728
    Listeriaceae.Listeria.Linnocua    ring_alpha    3    0.622910173385
    Listeriaceae.Listeria.Lmonocytogenes    ring_alpha    3    0.952569768174
    Listeriaceae.Listeria.Lseeligeri    ring_alpha    3    0.354875635794
    Listeriaceae.Listeria.Lwelshimeri    ring_alpha    3    0.692837888937
    Paenibacillaceae.Brevibacillus.Bbrevis    ring_alpha    3    0.580492537793
    Paenibacillaceae.Brevibacillus.Blaterosporus    ring_alpha    3    0.67891660613
    Paenibacillaceae.Paenibacillus.Pcurdlanolyticus    ring_alpha    3    0.0180110682393
    Paenibacillaceae.Paenibacillus.Plarvae    ring_alpha    3    0.953608677163
    Paenibacillaceae.Paenibacillus.Pmucilaginosus    ring_alpha    3    0.358675673023
    Paenibacillaceae.Paenibacillus.Ppolymyxa    ring_alpha    3    0.486438688396
    Paenibacillaceae.Paenibacillus.Pvortex    ring_alpha    3    0.186068756014
    Staphylococcaceae.Macrococcus.Mcaseolyticus    ring_alpha    3    0.725693055143
    Staphylococcaceae.Staphylococcus.Saureus    ring_alpha    3    0.374342186447
    Staphylococcaceae.Staphylococcus.Scapitis    ring_alpha    3    0.510175055083
    Staphylococcaceae.Staphylococcus.Scaprae    ring_alpha    3    0.948314742048
    Staphylococcaceae.Staphylococcus.Scarnosus    ring_alpha    3    0.935701022727
    Staphylococcaceae.Staphylococcus.Sepidermidis    ring_alpha    3    0.0938645581046
    Staphylococcaceae.Staphylococcus.Shaemolyticus    ring_alpha    3    0.728085338534
    Staphylococcaceae.Staphylococcus.Shominis    ring_alpha    3    0.741611869641
    Staphylococcaceae.Staphylococcus.Slugdunensis    ring_alpha    3    0.969166259753
    Staphylococcaceae.Staphylococcus.Spseudintermedius    ring_alpha    3    0.437648811318
    Staphylococcaceae.Staphylococcus.Ssaprophyticus    ring_alpha    3    0.781992078475
    Staphylococcaceae.Staphylococcus.Swarneri    ring_alpha    3    0.867129362962
    Bacillaceae.Anoxybacillus.Aflavithermus    ring_color    3    #AA00AA
    Bacillaceae.Bacillus.Bamyloliquefaciens    ring_color    3    #AA00AA
    Bacillaceae.Bacillus.Banthracis    ring_color    3    #AA00AA
    Bacillaceae.Bacillus.Batrophaeus    ring_color    3    #AA00AA
    Bacillaceae.Bacillus.Bcellulosilyticus    ring_color    3    #AA00AA
    Bacillaceae.Bacillus.Bcereus    ring_color    3    #AA00AA
    Bacillaceae.Bacillus.Bclausii    ring_color    3    #AA00AA
    Bacillaceae.Bacillus.Bcoagulans    ring_color    3    #AA00AA
    Bacillaceae.Bacillus.Bcoahuilensis    ring_color    3    #AA00AA
    Bacillaceae.Bacillus.Bhalodurans    ring_color    3    #AA00AA
    Bacillaceae.Bacillus.Blicheniformis    ring_color    3    #AA00AA
    Bacillaceae.Bacillus.Bmegaterium    ring_color    3    #AA00AA
    Bacillaceae.Bacillus.Bmycoides    ring_color    3    #AA00AA
    Bacillaceae.Bacillus.Bpseudofirmus    ring_color    3    #AA00AA
    Bacillaceae.Bacillus.Bpseudomycoides    ring_color    3    #AA00AA
    Bacillaceae.Bacillus.Bpumilus    ring_color    3    #AA00AA
    Bacillaceae.Bacillus.Bselenitireducens    ring_color    3    #AA00AA
    Bacillaceae.Bacillus.Bsubtilis    ring_color    3    #AA00AA
    Bacillaceae.Bacillus.Bthuringiensis    ring_color    3    #AA00AA
    Bacillaceae.Bacillus.Bweihenstephanensis    ring_color    3    #AA00AA
    Bacillaceae.Caldalkalibacillus.Cthermarum    ring_color    3    #AA00AA
    Bacillaceae.Geobacillus.Gkaustophilus    ring_color    3    #AA00AA
    Bacillaceae.Geobacillus.Gthermodenitrificans    ring_color    3    #AA00AA
    Bacillaceae.Geobacillus.Gthermoglucosidasius    ring_color    3    #AA00AA
    Bacillaceae.Lysinibacillus.Lfusiformis    ring_color    3    #AA00AA
    Bacillaceae.Lysinibacillus.Lsphaericus    ring_color    3    #AA00AA
    Bacillaceae.Oceanobacillus.Oiheyensis    ring_color    3    #AA00AA
    Listeriaceae.Listeria.Lgrayi    ring_color    3    #AA00AA
    Listeriaceae.Listeria.Linnocua    ring_color    3    #AA00AA
    Listeriaceae.Listeria.Lmonocytogenes    ring_color    3    #AA00AA
    Listeriaceae.Listeria.Lseeligeri    ring_color    3    #AA00AA
    Listeriaceae.Listeria.Lwelshimeri    ring_color    3    #AA00AA
    Paenibacillaceae.Brevibacillus.Bbrevis    ring_color    3    #AA00AA
    Paenibacillaceae.Brevibacillus.Blaterosporus    ring_color    3    #AA00AA
    Paenibacillaceae.Paenibacillus.Pcurdlanolyticus    ring_color    3    #AA00AA
    Paenibacillaceae.Paenibacillus.Plarvae    ring_color    3    #AA00AA
    Paenibacillaceae.Paenibacillus.Pmucilaginosus    ring_color    3    #AA00AA
    Paenibacillaceae.Paenibacillus.Ppolymyxa    ring_color    3    #AA00AA
    Paenibacillaceae.Paenibacillus.Pvortex    ring_color    3    #AA00AA
    Staphylococcaceae.Macrococcus.Mcaseolyticus    ring_color    3    #AA00AA
    Staphylococcaceae.Staphylococcus.Saureus    ring_color    3    #AA00AA
    Staphylococcaceae.Staphylococcus.Scapitis    ring_color    3    #AA00AA
    Staphylococcaceae.Staphylococcus.Scaprae    ring_color    3    #AA00AA
    Staphylococcaceae.Staphylococcus.Scarnosus    ring_color    3    #AA00AA
    Staphylococcaceae.Staphylococcus.Sepidermidis    ring_color    3    #AA00AA
    Staphylococcaceae.Staphylococcus.Shaemolyticus    ring_color    3    #AA00AA
    Staphylococcaceae.Staphylococcus.Shominis    ring_color    3    #AA00AA
    Staphylococcaceae.Staphylococcus.Slugdunensis    ring_color    3    #AA00AA
    Staphylococcaceae.Staphylococcus.Spseudintermedius    ring_color    3    #AA00AA
    Staphylococcaceae.Staphylococcus.Ssaprophyticus    ring_color    3    #AA00AA
    Staphylococcaceae.Staphylococcus.Swarneri    ring_color    3    #AA00AA
    Bacillaceae.Anoxybacillus.Aflavithermus    ring_alpha    4    0.0164337819514
    Bacillaceae.Bacillus.Bamyloliquefaciens    ring_alpha    4    0.961779754562
    Bacillaceae.Bacillus.Banthracis    ring_alpha    4    0.0911294036676
    Bacillaceae.Bacillus.Batrophaeus    ring_alpha    4    0.214683813052
    Bacillaceae.Bacillus.Bcellulosilyticus    ring_alpha    4    0.1835464929
    Bacillaceae.Bacillus.Bcereus    ring_alpha    4    0.649839771735
    Bacillaceae.Bacillus.Bclausii    ring_alpha    4    0.508572486958
    Bacillaceae.Bacillus.Bcoagulans    ring_alpha    4    0.54485221387
    Bacillaceae.Bacillus.Bcoahuilensis    ring_alpha    4    0.011849863671
    Bacillaceae.Bacillus.Bhalodurans    ring_alpha    4    0.494163373827
    Bacillaceae.Bacillus.Blicheniformis    ring_alpha    4    0.0037027183784
    Bacillaceae.Bacillus.Bmegaterium    ring_alpha    4    0.944619736609
    Bacillaceae.Bacillus.Bmycoides    ring_alpha    4    0.740793384052
    Bacillaceae.Bacillus.Bpseudofirmus    ring_alpha    4    0.679054870785
    Bacillaceae.Bacillus.Bpseudomycoides    ring_alpha    4    0.65485119746
    Bacillaceae.Bacillus.Bpumilus    ring_alpha    4    0.696989248748
    Bacillaceae.Bacillus.Bselenitireducens    ring_alpha    4    0.250910763296
    Bacillaceae.Bacillus.Bsubtilis    ring_alpha    4    0.603110791976
    Bacillaceae.Bacillus.Bthuringiensis    ring_alpha    4    0.768995251147
    Bacillaceae.Bacillus.Bweihenstephanensis    ring_alpha    4    0.382492089443
    Bacillaceae.Caldalkalibacillus.Cthermarum    ring_alpha    4    0.202515841523
    Bacillaceae.Geobacillus.Gkaustophilus    ring_alpha    4    0.604966298977
    Bacillaceae.Geobacillus.Gthermodenitrificans    ring_alpha    4    0.271415944271
    Bacillaceae.Geobacillus.Gthermoglucosidasius    ring_alpha    4    0.729366061868
    Bacillaceae.Lysinibacillus.Lfusiformis    ring_alpha    4    0.281874921267
    Bacillaceae.Lysinibacillus.Lsphaericus    ring_alpha    4    0.986149233417
    Bacillaceae.Oceanobacillus.Oiheyensis    ring_alpha    4    0.0868426043474
    Listeriaceae.Listeria.Lgrayi    ring_alpha    4    0.581618564755
    Listeriaceae.Listeria.Linnocua    ring_alpha    4    0.587717564353
    Listeriaceae.Listeria.Lmonocytogenes    ring_alpha    4    0.520464993313
    Listeriaceae.Listeria.Lseeligeri    ring_alpha    4    0.689907782867
    Listeriaceae.Listeria.Lwelshimeri    ring_alpha    4    0.432283970377
    Paenibacillaceae.Brevibacillus.Bbrevis    ring_alpha    4    0.713859589198
    Paenibacillaceae.Brevibacillus.Blaterosporus    ring_alpha    4    0.91882698904
    Paenibacillaceae.Paenibacillus.Pcurdlanolyticus    ring_alpha    4    0.0448745597998
    Paenibacillaceae.Paenibacillus.Plarvae    ring_alpha    4    0.702703981052
    Paenibacillaceae.Paenibacillus.Pmucilaginosus    ring_alpha    4    0.365023286887
    Paenibacillaceae.Paenibacillus.Ppolymyxa    ring_alpha    4    0.73860888919
    Paenibacillaceae.Paenibacillus.Pvortex    ring_alpha    4    0.905904555893
    Staphylococcaceae.Macrococcus.Mcaseolyticus    ring_alpha    4    0.252754272893
    Staphylococcaceae.Staphylococcus.Saureus    ring_alpha    4    0.483919418674
    Staphylococcaceae.Staphylococcus.Scapitis    ring_alpha    4    0.652801998863
    Staphylococcaceae.Staphylococcus.Scaprae    ring_alpha    4    0.726258452089
    Staphylococcaceae.Staphylococcus.Scarnosus    ring_alpha    4    0.833070576852
    Staphylococcaceae.Staphylococcus.Sepidermidis    ring_alpha    4    0.645235993575
    Staphylococcaceae.Staphylococcus.Shaemolyticus    ring_alpha    4    0.470807178843
    Staphylococcaceae.Staphylococcus.Shominis    ring_alpha    4    0.777865349824
    Staphylococcaceae.Staphylococcus.Slugdunensis    ring_alpha    4    0.00619809441301
    Staphylococcaceae.Staphylococcus.Spseudintermedius    ring_alpha    4    0.652324807659
    Staphylococcaceae.Staphylococcus.Ssaprophyticus    ring_alpha    4    0.580610729368
    Staphylococcaceae.Staphylococcus.Swarneri    ring_alpha    4    0.243468671906
    Bacillaceae.Anoxybacillus.Aflavithermus    ring_color    4    #00AAAA
    Bacillaceae.Bacillus.Bamyloliquefaciens    ring_color    4    #00AAAA
    Bacillaceae.Bacillus.Banthracis    ring_color    4    #00AAAA
    Bacillaceae.Bacillus.Batrophaeus    ring_color    4    #00AAAA
    Bacillaceae.Bacillus.Bcellulosilyticus    ring_color    4    #00AAAA
    Bacillaceae.Bacillus.Bcereus    ring_color    4    #00AAAA
    Bacillaceae.Bacillus.Bclausii    ring_color    4    #00AAAA
    Bacillaceae.Bacillus.Bcoagulans    ring_color    4    #00AAAA
    Bacillaceae.Bacillus.Bcoahuilensis    ring_color    4    #00AAAA
    Bacillaceae.Bacillus.Bhalodurans    ring_color    4    #00AAAA
    Bacillaceae.Bacillus.Blicheniformis    ring_color    4    #00AAAA
    Bacillaceae.Bacillus.Bmegaterium    ring_color    4    #00AAAA
    Bacillaceae.Bacillus.Bmycoides    ring_color    4    #00AAAA
    Bacillaceae.Bacillus.Bpseudofirmus    ring_color    4    #00AAAA
    Bacillaceae.Bacillus.Bpseudomycoides    ring_color    4    #00AAAA
    Bacillaceae.Bacillus.Bpumilus    ring_color    4    #00AAAA
    Bacillaceae.Bacillus.Bselenitireducens    ring_color    4    #00AAAA
    Bacillaceae.Bacillus.Bsubtilis    ring_color    4    #00AAAA
    Bacillaceae.Bacillus.Bthuringiensis    ring_color    4    #00AAAA
    Bacillaceae.Bacillus.Bweihenstephanensis    ring_color    4    #00AAAA
    Bacillaceae.Caldalkalibacillus.Cthermarum    ring_color    4    #00AAAA
    Bacillaceae.Geobacillus.Gkaustophilus    ring_color    4    #00AAAA
    Bacillaceae.Geobacillus.Gthermodenitrificans    ring_color    4    #00AAAA
    Bacillaceae.Geobacillus.Gthermoglucosidasius    ring_color    4    #00AAAA
    Bacillaceae.Lysinibacillus.Lfusiformis    ring_color    4    #00AAAA
    Bacillaceae.Lysinibacillus.Lsphaericus    ring_color    4    #00AAAA
    Bacillaceae.Oceanobacillus.Oiheyensis    ring_color    4    #00AAAA
    Listeriaceae.Listeria.Lgrayi    ring_color    4    #00AAAA
    Listeriaceae.Listeria.Linnocua    ring_color    4    #00AAAA
    Listeriaceae.Listeria.Lmonocytogenes    ring_color    4    #00AAAA
    Listeriaceae.Listeria.Lseeligeri    ring_color    4    #00AAAA
    Listeriaceae.Listeria.Lwelshimeri    ring_color    4    #00AAAA
    Paenibacillaceae.Brevibacillus.Bbrevis    ring_color    4    #00AAAA
    Paenibacillaceae.Brevibacillus.Blaterosporus    ring_color    4    #00AAAA
    Paenibacillaceae.Paenibacillus.Pcurdlanolyticus    ring_color    4    #00AAAA
    Paenibacillaceae.Paenibacillus.Plarvae    ring_color    4    #00AAAA
    Paenibacillaceae.Paenibacillus.Pmucilaginosus    ring_color    4    #00AAAA
    Paenibacillaceae.Paenibacillus.Ppolymyxa    ring_color    4    #00AAAA
    Paenibacillaceae.Paenibacillus.Pvortex    ring_color    4    #00AAAA
    Staphylococcaceae.Macrococcus.Mcaseolyticus    ring_color    4    #00AAAA
    Staphylococcaceae.Staphylococcus.Saureus    ring_color    4    #00AAAA
    Staphylococcaceae.Staphylococcus.Scapitis    ring_color    4    #00AAAA
    Staphylococcaceae.Staphylococcus.Scaprae    ring_color    4    #00AAAA
    Staphylococcaceae.Staphylococcus.Scarnosus    ring_color    4    #00AAAA
    Staphylococcaceae.Staphylococcus.Sepidermidis    ring_color    4    #00AAAA
    Staphylococcaceae.Staphylococcus.Shaemolyticus    ring_color    4    #00AAAA
    Staphylococcaceae.Staphylococcus.Shominis    ring_color    4    #00AAAA
    Staphylococcaceae.Staphylococcus.Slugdunensis    ring_color    4    #00AAAA
    Staphylococcaceae.Staphylococcus.Spseudintermedius    ring_color    4    #00AAAA
    Staphylococcaceae.Staphylococcus.Ssaprophyticus    ring_color    4    #00AAAA
    Staphylococcaceae.Staphylococcus.Swarneri    ring_color    4    #00AAAA
    Bacillaceae.Anoxybacillus.Aflavithermus    ring_height    5    2.48900854747
    Bacillaceae.Bacillus.Bamyloliquefaciens    ring_height    5    2.5569451352
    Bacillaceae.Bacillus.Banthracis    ring_height    5    1.4616581923
    Bacillaceae.Bacillus.Batrophaeus    ring_height    5    1.5214251868
    Bacillaceae.Bacillus.Bcellulosilyticus    ring_height    5    0.275406475474
    Bacillaceae.Bacillus.Bcereus    ring_height    5    3.96420929693
    Bacillaceae.Bacillus.Bclausii    ring_height    5    0.36682224696
    Bacillaceae.Bacillus.Bcoagulans    ring_height    5    3.11304018594
    Bacillaceae.Bacillus.Bcoahuilensis    ring_height    5    3.17186920433
    Bacillaceae.Bacillus.Bhalodurans    ring_height    5    1.03261323231
    Bacillaceae.Bacillus.Blicheniformis    ring_height    5    2.84479580061
    Bacillaceae.Bacillus.Bmegaterium    ring_height    5    1.97722308257
    Bacillaceae.Bacillus.Bmycoides    ring_height    5    2.66122684072
    Bacillaceae.Bacillus.Bpseudofirmus    ring_height    5    1.43290815777
    Bacillaceae.Bacillus.Bpseudomycoides    ring_height    5    1.11687288226
    Bacillaceae.Bacillus.Bpumilus    ring_height    5    1.08510776094
    Bacillaceae.Bacillus.Bselenitireducens    ring_height    5    2.77859614711
    Bacillaceae.Bacillus.Bsubtilis    ring_height    5    0.554574632132
    Bacillaceae.Bacillus.Bthuringiensis    ring_height    5    1.57378483828
    Bacillaceae.Bacillus.Bweihenstephanensis    ring_height    5    2.70028276238
    Bacillaceae.Caldalkalibacillus.Cthermarum    ring_height    5    1.86166458022
    Bacillaceae.Geobacillus.Gkaustophilus    ring_height    5    0.0242900869783
    Bacillaceae.Geobacillus.Gthermodenitrificans    ring_height    5    3.07841560635
    Bacillaceae.Geobacillus.Gthermoglucosidasius    ring_height    5    3.46510209264
    Bacillaceae.Lysinibacillus.Lfusiformis    ring_height    5    1.35283141925
    Bacillaceae.Lysinibacillus.Lsphaericus    ring_height    5    3.92974800987
    Bacillaceae.Oceanobacillus.Oiheyensis    ring_height    5    2.28533114154
    Listeriaceae.Listeria.Lgrayi    ring_height    5    0.818507572602
    Listeriaceae.Listeria.Linnocua    ring_height    5    0.800083345466
    Listeriaceae.Listeria.Lmonocytogenes    ring_height    5    0.978937868742
    Listeriaceae.Listeria.Lseeligeri    ring_height    5    0.892990893608
    Listeriaceae.Listeria.Lwelshimeri    ring_height    5    2.52510303764
    Paenibacillaceae.Brevibacillus.Bbrevis    ring_height    5    1.94634642846
    Paenibacillaceae.Brevibacillus.Blaterosporus    ring_height    5    2.53149220001
    Paenibacillaceae.Paenibacillus.Pcurdlanolyticus    ring_height    5    0.617175345723
    Paenibacillaceae.Paenibacillus.Plarvae    ring_height    5    1.49321243619
    Paenibacillaceae.Paenibacillus.Pmucilaginosus    ring_height    5    0.0817469468168
    Paenibacillaceae.Paenibacillus.Ppolymyxa    ring_height    5    3.26055825675
    Paenibacillaceae.Paenibacillus.Pvortex    ring_height    5    2.50175369758
    Staphylococcaceae.Macrococcus.Mcaseolyticus    ring_height    5    2.6642090736
    Staphylococcaceae.Staphylococcus.Saureus    ring_height    5    1.21391731853
    Staphylococcaceae.Staphylococcus.Scapitis    ring_height    5    0.92038173113
    Staphylococcaceae.Staphylococcus.Scaprae    ring_height    5    3.22193378354
    Staphylococcaceae.Staphylococcus.Scarnosus    ring_height    5    2.59751672494
    Staphylococcaceae.Staphylococcus.Sepidermidis    ring_height    5    0.365700208191
    Staphylococcaceae.Staphylococcus.Shaemolyticus    ring_height    5    1.34748130999
    Staphylococcaceae.Staphylococcus.Shominis    ring_height    5    0.0961524114391
    Staphylococcaceae.Staphylococcus.Slugdunensis    ring_height    5    2.02393979902
    Staphylococcaceae.Staphylococcus.Spseudintermedius    ring_height    5    1.94654560527
    Staphylococcaceae.Staphylococcus.Ssaprophyticus    ring_height    5    2.75289926136
    Staphylococcaceae.Staphylococcus.Swarneri    ring_height    5    2.39465498028
    
    
    Bacillaceae.Bacillus.Bsubtilis    clade_marker_label    65
    Staphylococcaceae.Staphylococcus.Saureus    clade_marker_label    17
    Bacillaceae.Bacillus.Banthracis    clade_marker_label    x    
    Bacillaceae.Bacillus.Banthracis    clade_marker_font_color    w
    Bacillaceae.Bacillus.Banthracis    clade_marker_edge_color    b
    Bacillaceae.Lysinibacillus.Lfusiformis    clade_marker_label    156
    Bacillaceae.Lysinibacillus.Lfusiformis    clade_marker_edge_color    b
    Bacillaceae.Oceanobacillus.Oiheyensis    clade_marker_label    18
    Bacillaceae.Oceanobacillus.Oiheyensis    clade_marker_color    k
    Bacillaceae.Oceanobacillus.Oiheyensis    clade_marker_font_color    w
    annot_3.txt

    四、输入文件的处理

    经过以上学习,已经大致了解了 GraPhlan 图的构成,以及 options 的内容。但是,一直有一个疑惑盘卧于心:如果数据量小,我可以手动写入注释文件,那如果数据量很大呢?要知道 Meta 注释的结果可能上万呀!经过各种检索,最后终于在 bitbucket 中找到了一个脚本 export2graphlan.py。可以根据物种样本丰度矩阵,来生成对应的 tree.txt 和 annot.txt(tree.txt 即上文中的 guide.txt)

    网址:https://bitbucket.org/CibioCM/export2graphlan/src/default/

    由于还没仔细研究这个脚本,我就在这里简单的举个例子,以最近分析的一个 Meta 结果为输入文件:(这里我是用的是“管道符”作为分隔符,没有使用“点”,也是可以的。)

    ID    SRS014459-Stool_profile    SRS014464-Anterior_nares_profile    SRS014470-Tongue_dorsum_profile    SRS014472-Buccal_mucosa_profile
    #SampleID     TKS    TMS    PTS    KTS
    k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa    0    0    2.218786516    20.10325925
    k__Bacteria|p__Candidatus Moranbacteria|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Candidatus Moranbacteria bacterium RBG_13_45_13    0    0    0    7.310276093
    k__Bacteria    0    0    0    9.278427348
    k__Bacteria|p__Acidobacteria|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified    0    0    0    7.389306104
    k__Bacteria|p__Chloroflexi    0    0    0    13.67021629
    k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobacteraceae|g__Desulfococcus|s__Desulfococcus multivorans    0    0    0    5.960850128
    k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__Actinobacteria bacterium    0    0    0    7.53872222
    k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhizobiales|f__Cohaesibacteraceae|g__Cohaesibacter    0    0    0    11.39184691
    k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Pseudoruegeria|s__Pseudoruegeria lutimaris    0    0    0    7.16969386
    k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobacteraceae|g__Unclassified|s__Desulfobacteraceae bacterium    0    0    0    14.23980864
    k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chloroflexi bacterium RBG_16_70_13    0    0    0    13.14443874
    k__Bacteria|p__Chloroflexi|c__Anaerolineae    0    13.68106333    2.112284763    8.202129776
    k__Bacteria|p__Acidobacteria|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Acidobacteria bacterium    0    0    0    29.01696855
    k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhizobiales|f__Rhizobiaceae|g__Rhizobium|s__Rhizobium etli    0    0    0    12.84794764
    k__Bacteria|p__Unclassified|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__bacterium HR39    0.724322421    0    0    10.29383757
    k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae    0    0    0    5.759922595
    k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria    0    0    0    14.54278329
    k__Bacteria|p__Ignavibacteriae|c__Ignavibacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__Ignavibacteria bacterium RBG_13_36_8    0    0    0    10.05162963
    k__Unclassified|p__Unclassified|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__uncultured prokaryote    0    0    0    9.685375916
    k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Draconibacterium    0    0    0    10.88393017
    k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__SAR86 cluster bacterium    0    0    0    8.946476632
    k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhizobiales|f__Unclassified|g__Methyloceanibacter|s__Methyloceanibacter marginalis    0    0    0    9.764440209
    k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Cellulomonadaceae    1.748909409    0    3.840517751    16.15571016
    k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhizobiales    0    0    0    12.65760768
    k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Syntrophobacterales|f__Unclassified|g__Unclassified|s__Syntrophobacterales bacterium RBG_19FT_COMBO_59_10    0    0    0    12.89643047
    k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides    0    0    0    13.22924157
    k__Bacteria|p__Actinobacteria|c__Acidimicrobiia|o__Acidimicrobiales|f__Ilumatobacteraceae    0    0    0    8.175966682
    k__Bacteria|p__Actinobacteria|c__Thermoleophilia|o__Solirubrobacterales|f__Patulibacteraceae|g__Patulibacter|s__Patulibacter minatonensis    0    0    0    8.41762087
    k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chloroflexi bacterium    0    0    0    12.2853251
    k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chloroflexi bacterium RBG_16_52_11    0    0    0    11.90192961
    k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae    0    0    0    9.526283131
    k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Lysobacter    0    0    0    8.543885183
    k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Lysobacter|s__Lysobacter maris    1.466311242    0    0    8.33549774
    k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Streptosporangiales|f__Thermomonosporaceae|g__Thermomonospora|s__Thermomonospora curvata    0    0    0    34.67083842
    k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Streptosporangiales|f__Streptosporangiaceae|g__Thermoactinospora|s__Thermoactinospora rubra    0    0    0    20.59686607
    k__Bacteria|p__Acidobacteria|c__Solibacteres|o__Solibacterales|f__Solibacteraceae|g__Candidatus Solibacter|s__Candidatus Solibacter usitatus    0    0    0    25.93679431
    k__Bacteria|p__Unclassified|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__bacterium    0    0    2.490901843    4.836161424
    k__Bacteria|p__Acidobacteria|c__Solibacteres|o__Solibacterales|f__Solibacteraceae|g__Candidatus Sulfopaludibacter|s__Candidatus Sulfopaludibacter sp. SbA3    0    0    0    21.90739791
    k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chloroflexi bacterium RBG_16_69_14    0.81516964    2.318824293    0    8.109450343
    k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chloroflexi bacterium CSP1-4    0    0    0    8.67399511
    k__Bacteria|p__Proteobacteria|c__Candidatus Muproteobacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__Candidatus Muproteobacteria bacterium RIFCSPLOWO2_01_FULL_60_18    0    0    0    5.817113316
    k__Archaea|p__Thaumarchaeota|c__Nitrososphaeria|o__Nitrososphaerales|f__Nitrososphaeraceae|g__Candidatus Nitrosocosmicus|s__Candidatus Nitrosocosmicus oleophilus    0    0    1.307106908    16.0726553
    k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae    0    0    0    16.64711153
    k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__delta proteobacterium MLMS-1    0    0    0    23.18441205
    k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus    0    0    0    21.67229412
    k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Intrasporangiaceae|g__Phycicoccus    0    0    0    20.59542944
    k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Mycobacteriaceae|g__Mycobacterium    0    0    0    17.37739359
    k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chloroflexi bacterium HGW-Chloroflexi-8    0    0    0    27.70989789
    k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhizobiales|f__Hyphomicrobiaceae|g__Rhodoplanes|s__Rhodoplanes sp. Z2-YC6860    0    0    0    20.55671623
    k__Bacteria|p__Proteobacteria|c__Betaproteobacteria    0    0    0    13.80829929
    k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chloroflexi bacterium HGW-Chloroflexi-6    0    0    0    15.83063195
    k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Haloferacales|f__Haloferacaceae|g__Halobellus|s__Halobellus limi    0    0    0    7.901859129
    k__Bacteria|p__Chlorobi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chlorobi bacterium OLB5    0.726510706    0    0    11.35743045
    k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria    0    0    0    33.09793359
    k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__uncultured Chloroflexi bacterium    0    0    0    7.594564607
    k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter|s__Arthrobacter sp. U41    0    0    0    9.672322849
    k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhizobiales|f__Unclassified|g__Bauldia|s__Bauldia litoralis    0    0    0    7.811552167
    k__Bacteria|p__Chloroflexi|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Anaerolinea|s__Anaerolinea thermolimosa    0    0    0    5.339928239
    k__Bacteria|p__Chloroflexi|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Longilinea|s__Longilinea arvoryzae    0    0    0    12.65760768
    k__Bacteria|p__Bacteroidetes|c__Cytophagia|o__Cytophagales|f__Cyclobacteriaceae|g__Algoriphagus    0    0    0    11.61304782
    k__Bacteria|p__candidate division NC10|c__Unclassified|o__Unclassified|f__Unclassified|g__Candidatus Methylomirabilis    0    0    0    11.39184691
    k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Actinomycetospora|s__Actinomycetospora cinnamomea    0    0    0    5.960850128
    k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__marine actinobacterium MedAcidi-G2B    0    0    0    11.94948977
    k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobacteraceae|g__Desulfobacter|s__Desulfobacter curvatus    1.422929253    0    0    24.26665614
    k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis    1.64708934    0    0    14.04474277
    k__Bacteria|p__Chloroflexi|c__Anaerolineae|o__Anaerolineales|f__Unclassified|g__Unclassified|s__Anaerolineales bacterium    0    4.023842156    3.106301122    6.030977776
    k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobacteraceae|g__Desulfatitalea|s__Desulfatitalea sp. BRH_c12    0    0    0    14.44036932
    k__Bacteria|p__Actinobacteria    0    0    0    8.993563351
    Unclassified    0    0    0    12.52506728
    k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Unclassified|f__Unclassified|g__Unclassified    0    0    0    10.05162963
    k__Bacteria|p__Proteobacteria    0    0    0    33.39629388
    k__Bacteria|p__Ignavibacteriae|c__Ignavibacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__Ignavibacteria bacterium RBG_16_34_14    0    0    0    13.20793845
    table.txt

    目前遇到的需要去除的特殊字符:

    1. 如果使用了其他分隔符,“点”是不可以出现的,否则会导致分割出错
    2. (class) 也不可以

    执行命令 work.sh:

    1 source /software/graphlan/activate.sh
    2 export2graphlan.py --skip_rows 1,2 -i table.txt --tree tree.txt --annotation annot.txt --most_abundant 40 --abundance_threshold 1 --least_biomarkers 10 --annotations 3,4,5,6 --external_annotations 7 --min_clade_size 1
    3 graphlan_annotate.py --annot annot.txt tree.txt abundance.xml
    4 graphlan.py --dpi 300 abundance.xml abundance.png --size 12

    得到结果:

    转载请注明出处:https://www.cnblogs.com/Shinamy/p/10905115.html

  • 相关阅读:
    e666. 创建缓冲图像
    e670. 缓冲图像转换为图像
    e680. 使三元色图像变明变暗
    e659. 缩放,剪取,移动,翻转图形
    e656. 创建基本图形
    e657. 用直线和曲线绘制图形
    e658. 组合图形
    e655. 混合风格的文本
    e654. 获得文本的缩略图
    e652. Getting the Font Faces for a Font Family
  • 原文地址:https://www.cnblogs.com/Shinamy/p/10905115.html
Copyright © 2011-2022 走看看