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notebook: update figure S11
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matinnuhamunada committed Jun 15, 2023
1 parent 58de61f commit 0e54576
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Showing 21 changed files with 11,151 additions and 11,115 deletions.
2 changes: 1 addition & 1 deletion 24_FigS11_staphylobactin_gggenomes.R.ipynb
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" values=c('#f94144', '#f3722c', '#f8961e', '#f9c74f', '#90be6d', '#43aa8b', '#577590', \n",
" 'gray', 'white')) +\n",
" scale_color_viridis_d(\"Blast hits & Features\", direction = -1) +\n",
" scale_linetype(\"Graphs\") + theme(legend.position=\"none\")\n",
" scale_linetype(\"Graphs\") + theme(legend.position=\"right\")\n",
"\n",
"fig <- t3 + scale_y_continuous(expand=c(0.01,0.7,0.01,0.7)) + p2 %>% pick_by_tree(t2) + plot_layout(widths = c(2,2))\n",
"ggsave(file=outfile_svg, plot=fig, device=svglite, width=2800, height=1800, units=\"px\")\n",
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468 changes: 234 additions & 234 deletions assets/data/Figure_S11/msa/Staphylobactin/core_BGC_concat.fasta

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468 changes: 234 additions & 234 deletions assets/data/Figure_S11/msa/Staphylobactin/core_BGC_concat_clean.fasta

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(((NZ_CP040605.1.region017:0.011151809,NZ_CP031142.1.region007:0.012888998):0.011426795,((NZ_CP061007.1.region003:0.00045580487,NZ_PJNB01000001.1.region028:-0.0001454719):0.00046192866,NZ_GL877881.1.region003:0.0036161868):0.032435406):0.084254071,NZ_JACHIW010000002.1.region002:0.15212503,(BGC0000943.region001:1.342497,(NZ_JAGPXE010000002.1.region001:0.089138456,NZ_FOZX01000003.1.region003:0.11087934):0.029545546):0.084960841);
(((NZ_GL877881.1.region003:0.0036160131,(NZ_PJNB01000001.1.region028:-0.00014538996,NZ_CP061007.1.region003:0.00045572288):0.00046209292):0.032434799,(NZ_CP040605.1.region017:0.01115183,NZ_CP031142.1.region007:0.012888804):0.011426458):0.084249109,((NZ_FOZX01000003.1.region003:0.11087352,NZ_JAGPXE010000002.1.region001:0.089135125):0.029541016,BGC0000943.region001:1.3423543):0.084953099,NZ_JACHIW010000002.1.region002:0.15211514);
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508 changes: 255 additions & 253 deletions assets/data/Figure_S11/msa/Staphylobactin/core_BGC_concat_clean.fasta.log

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NZ_CP040605.1.region017 0.0000000 0.0566446 1.5228644 0.2617784 0.0562739 0.0240408 0.3329252 0.0595328 0.3508967
NZ_CP061007.1.region003 0.0566446 0.0000000 1.5283462 0.2642563 0.0003103 0.0566578 0.3294190 0.0043912 0.3520297
BGC0000943.region001 1.5228644 1.5283462 0.0000000 1.5545554 1.5266832 1.5238410 1.4623109 1.5265597 1.4817917
NZ_JACHIW010000002.1.region002 0.2617784 0.2642563 1.5545554 0.0000000 0.2636891 0.2676823 0.3782949 0.2680816 0.4050406
NZ_PJNB01000001.1.region028 0.0562739 0.0003103 1.5266832 0.2636891 0.0000000 0.0562889 0.3287891 0.0040754 0.3513775
NZ_CP031142.1.region007 0.0240408 0.0566578 1.5238410 0.2676823 0.0562889 0.0000000 0.3365761 0.0595316 0.3563127
NZ_JAGPXE010000002.1.region001 0.3329252 0.3294190 1.4623109 0.3782949 0.3287891 0.3365761 0.0000000 0.3328568 0.2000178
NZ_GL877881.1.region003 0.0595328 0.0043912 1.5265597 0.2680816 0.0040754 0.0595316 0.3328568 0.0000000 0.3559095
NZ_FOZX01000003.1.region003 0.3508967 0.3520297 1.4817917 0.4050406 0.3513775 0.3563127 0.2000178 0.3559095 0.0000000
NZ_GL877881.1.region003 0.0000000 0.3558851 1.5264044 0.0595317 0.0595305 0.3328346 0.0040754 0.2680660 0.0043912
NZ_FOZX01000003.1.region003 0.3558851 0.0000000 1.4816384 0.3508726 0.3562882 0.2000086 0.3513535 0.4050106 0.3520056
BGC0000943.region001 1.5264044 1.4816384 0.0000000 1.5227098 1.5236861 1.4621608 1.5265278 1.5543967 1.5281907
NZ_CP040605.1.region017 0.0595317 0.3508726 1.5227098 0.0000000 0.0240406 0.3329032 0.0562729 0.2617633 0.0566436
NZ_CP031142.1.region007 0.0595305 0.3562882 1.5236861 0.0240406 0.0000000 0.3365536 0.0562880 0.2676666 0.0566568
NZ_JAGPXE010000002.1.region001 0.3328346 0.2000086 1.4621608 0.3329032 0.3365536 0.0000000 0.3287675 0.3782684 0.3293973
NZ_PJNB01000001.1.region028 0.0040754 0.3513535 1.5265278 0.0562729 0.0562880 0.3287675 0.0000000 0.2636739 0.0003103
NZ_JACHIW010000002.1.region002 0.2680660 0.4050106 1.5543967 0.2617633 0.2676666 0.3782684 0.2636739 0.0000000 0.2642410
NZ_CP061007.1.region003 0.0043912 0.3520056 1.5281907 0.0566436 0.0566568 0.3293973 0.0003103 0.2642410 0.0000000
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(NZ_CP040605.1.region017:0.0121163241,(((NZ_CP061007.1.region003:0.0003150485,NZ_PJNB01000001.1.region028:0.0000009987):0.0003589735,NZ_GL877881.1.region003:0.0038639268):0.0269994528,((BGC0000943.region001:1.4417343098,(NZ_JAGPXE010000002.1.region001:0.0896078126,NZ_FOZX01000003.1.region003:0.1244890467):0.0786676160):0.0877577486,NZ_JACHIW010000002.1.region002:0.1671798207):0.0873810340):0.0206752592,NZ_CP031142.1.region007:0.0125783416);
(NZ_GL877881.1.region003:0.0038639585,((((NZ_FOZX01000003.1.region003:0.1245024744,NZ_JAGPXE010000002.1.region001:0.0895905875):0.0786657393,BGC0000943.region001:1.4416864124):0.0877557590,NZ_JACHIW010000002.1.region002:0.1671757385):0.0873797253,(NZ_CP040605.1.region017:0.0121163206,NZ_CP031142.1.region007:0.0125784011):0.0206753313):0.0269992809,(NZ_PJNB01000001.1.region028:0.0000009987,NZ_CP061007.1.region003:0.0003150548):0.0003589589);
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