From c81431edcda6587888bda8a8c35b1c37445a8a10 Mon Sep 17 00:00:00 2001 From: Adrien Taudiere Date: Tue, 12 Dec 2023 10:06:44 +0100 Subject: [PATCH 1/7] bugfix: retry to install mumu --- .github/workflows/test-coverage.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 97929b34..4eeea310 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -32,7 +32,7 @@ jobs: run: sudo apt-get install ncbi-blast+ - name: Install mumu - run: > + run: | git clone https://github.com/frederic-mahe/mumu.git \ && cd ./mumu/\ && make\ From 6ae157d0039e582b3fe697c69c948c3fcadcd4f2 Mon Sep 17 00:00:00 2001 From: Adrien Taudiere Date: Tue, 12 Dec 2023 10:07:05 +0100 Subject: [PATCH 2/7] better images for publication --- paper/figures_svg/table1_publication.svg | 5585 +++++++++++++++----- paper/figures_svg/tengeler_MiscMetabar.svg | 192 +- 2 files changed, 4233 insertions(+), 1544 deletions(-) diff --git a/paper/figures_svg/table1_publication.svg b/paper/figures_svg/table1_publication.svg index 6da525dc..276b69b7 100644 --- a/paper/figures_svg/table1_publication.svg +++ b/paper/figures_svg/table1_publication.svg @@ -7,8 +7,31 @@ width="541.73224" height="646.10156" viewBox="0 0 541.73224 646.10156" + sodipodi:docname="table1_publication.svg" + inkscape:version="1.2 (dc2aedaf03, 2022-05-15)" + xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape" + xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd" xmlns="http://www.w3.org/2000/svg" xmlns:svg="http://www.w3.org/2000/svg"> + - - + id="g11869" + clip-path="url(#clipPath11873)" /> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + d="M 184.911,489.256 H 441.0585" + style="fill:none;stroke:#333333;stroke-width:0.65253;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:10;stroke-dasharray:none;stroke-opacity:1" + id="path12019" /> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + d="M 184.911,318.895 H 441.0585" + style="fill:none;stroke:#333333;stroke-width:0.65253;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:10;stroke-dasharray:none;stroke-opacity:1" + id="path12063" /> + + + + + + d="M 184.911,295.516 H 441.0585" + style="fill:none;stroke:#333333;stroke-width:0.65253;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:10;stroke-dasharray:none;stroke-opacity:1" + id="path12071" /> + + + d="M 184.911,283.827 H 441.0585" + style="fill:none;stroke:#333333;stroke-width:0.65253;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:10;stroke-dasharray:none;stroke-opacity:1" + id="path12075" /> + + + d="M 184.911,272.137 H 441.0585" + style="fill:none;stroke:#333333;stroke-width:0.65253;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:10;stroke-dasharray:none;stroke-opacity:1" + id="path12079" /> + + + d="M 184.911,260.448 H 441.0585" + style="fill:none;stroke:#333333;stroke-width:0.65253;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:10;stroke-dasharray:none;stroke-opacity:1" + id="path12083" /> + + + d="M 184.911,248.758 H 441.0585" + style="fill:none;stroke:#000000;stroke-width:0.65253;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:10;stroke-dasharray:none;stroke-opacity:1" + id="path12087" /> + + + d="M 184.911,248.758 H 441.0585" + style="fill:none;stroke:#000000;stroke-width:0.65253;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:10;stroke-dasharray:none;stroke-opacity:1" + id="path12091" /> + + + + + + + + + + + + + + + + + + aria-label="Other packages" + transform="matrix(1,0,0,-1,363.016,708.151)" + id="text12103" + style="font-weight:bold;font-size:8.705px;font-family:'Liberation Sans';-inkscape-font-specification:LiberationSans-Bold"> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + d="m 17.228521,-3.8551928 q 0.221026,-0.3060352 0.595069,-0.4930567 0.378293,-0.1870215 0.794841,-0.1870215 0.765088,0 1.198638,0.6333228 0.4378,0.6290723 0.4378,1.6406885 0,1.0201171 -0.459053,1.70019525 -0.454802,0.67582763 -1.228391,0.67582763 -0.412297,0 -0.773589,-0.20402343 -0.357041,-0.20827393 -0.565315,-0.54831299 V 1.7512012 h -0.663076 v -6.18021 h 0.663076 z m 0,0.6588256 v 1.8404615 q 0.187022,0.37404292 0.505809,0.62482172 0.318786,0.25077881 0.658825,0.25077881 0.535562,0 0.850098,-0.50155761 0.318787,-0.50155762 0.318787,-1.24539302 0,-0.7650879 -0.301785,-1.2496436 -0.301785,-0.4845556 -0.841597,-0.4845556 -0.70133,0 -1.190137,0.7650878 z" + id="path1454" /> - - + d="m 24.87855,0 h -1.810708 v -5.423623 h -1.156133 v -0.5738159 h 1.819209 v 5.42362299 h 1.147632 z" + id="path1456" /> - - + d="m 28.689979,-4.535271 q 0.913855,0 1.453667,0.6375733 0.539812,0.6375732 0.539812,1.6789428 0,1.0498706 -0.539812,1.69169436 -0.539812,0.64182372 -1.453667,0.64182372 -0.918105,0 -1.457917,-0.63757323 Q 26.6965,-1.1646338 26.6965,-2.2187549 q 0,-1.0456201 0.539812,-1.6789428 0.539812,-0.6375733 1.453667,-0.6375733 z m 0,4.07196778 q 0.603569,0 0.952109,-0.51005859 0.34854,-0.51005859 0.34854,-1.23689209 0,-0.7650879 -0.344289,-1.2581445 -0.34429,-0.4930566 -0.95636,-0.4930566 -0.616321,0 -0.95636,0.4888061 -0.340039,0.4845557 -0.340039,1.262395 0,0.739585 0.34429,1.24539307 0.344289,0.50155761 0.952109,0.50155761 z" + id="path1458" /> - - + d="m 35.672683,-0.19977295 q -0.667327,0.30603516 -1.313401,0.30603516 -1.185886,0 -1.185886,-1.25389401 v -2.707561 h -0.850098 v -0.573816 h 0.850098 v -1.2113891 h 0.646074 v 1.2113891 h 1.504673 v 0.573816 H 33.81947 v 2.533291 q 0,0.40379634 0.17852,0.62907222 0.178521,0.22102538 0.484556,0.22102538 0.544062,0 1.075373,-0.24227782 z" + id="path1460" /> - - + d="m 41.75003,1.8957178 h -5.22385 v -0.556814 h 5.22385 z" + id="path1462" /> - - + d="m 46.169279,0 h -0.658825 q -0.08076,-0.26778076 -0.08076,-0.71408202 -0.565315,0.8288452 -1.538676,0.8288452 -0.493057,0 -0.871351,-0.34854003 -0.374042,-0.35279053 -0.374042,-0.90535395 0,-0.3272876 0.131765,-0.5780665 0.131765,-0.2507788 0.386794,-0.4207983 0.255029,-0.17427 0.620571,-0.2720312 0.365542,-0.1020118 0.8671,-0.1402661 l 0.743835,-0.059507 v -0.2125244 q 0,-1.1391308 -1.062622,-1.1391308 -0.250778,0 -0.637573,0.1105127 -0.382544,0.1062622 -0.658826,0.2550292 l -0.17427,-0.4760546 q 0.905354,-0.4633033 1.683194,-0.4633033 1.513174,0 1.513174,1.6024341 v 1.9042187 q 0,0.57806645 0.110512,1.0286182 z M 45.39569,-1.3134009 v -0.8033422 q -0.896853,0.080759 -1.232641,0.1530175 -0.331538,0.068008 -0.578067,0.2592798 -0.242277,0.191272 -0.242277,0.5185596 0,0.29753416 0.208274,0.48030515 0.208273,0.182771 0.531311,0.182771 0.35279,0 0.70133,-0.20827393 0.34854,-0.21252441 0.61207,-0.58231692 z" + id="path1464" /> - - + d="m 50.958729,0 h -1.810708 v -5.423623 h -1.156133 v -0.5738159 h 1.819209 v 5.42362299 h 1.147632 z" + id="path1466" /> - - + d="m 53.7547,-3.8551928 q 0.221025,-0.3060352 0.595068,-0.4930567 0.378294,-0.1870215 0.794842,-0.1870215 0.765087,0 1.198637,0.6333228 0.4378,0.6290723 0.4378,1.6406885 0,1.0201171 -0.459052,1.70019525 -0.454802,0.67582763 -1.228391,0.67582763 -0.412298,0 -0.773589,-0.20402343 Q 53.962974,-0.29753418 53.7547,-0.63757324 V 1.7512012 h -0.663076 v -6.18021 H 53.7547 Z m 0,0.6588256 v 1.8404615 q 0.187021,0.37404292 0.505808,0.62482172 0.318787,0.25077881 0.658826,0.25077881 0.535561,0 0.850097,-0.50155761 0.318787,-0.50155762 0.318787,-1.24539302 0,-0.7650879 -0.301785,-1.2496436 -0.301784,-0.4845556 -0.841596,-0.4845556 -0.701331,0 -1.190137,0.7650878 z" + id="path1468" /> - - + d="m 61.710359,0 h -0.663076 v -2.8393261 q 0,-0.5908179 -0.191272,-0.8543482 -0.187022,-0.2677807 -0.590818,-0.2677807 -0.60782,0 -1.3049,0.7565869 V 0 h -0.663076 v -5.9974389 h 0.663076 v 2.2187549 q 0.714082,-0.756587 1.504673,-0.756587 1.245393,0 1.245393,1.5046729 z" + id="path1470" /> - - + d="m 67.043871,0 h -0.658826 q -0.08076,-0.26778076 -0.08076,-0.71408202 -0.565315,0.8288452 -1.538677,0.8288452 -0.493056,0 -0.87135,-0.34854003 -0.374043,-0.35279053 -0.374043,-0.90535395 0,-0.3272876 0.131765,-0.5780665 0.131766,-0.2507788 0.386795,-0.4207983 0.255029,-0.17427 0.620571,-0.2720312 0.365542,-0.1020118 0.8671,-0.1402661 l 0.743835,-0.059507 v -0.2125244 q 0,-1.1391308 -1.062622,-1.1391308 -0.250779,0 -0.637573,0.1105127 -0.382544,0.1062622 -0.658826,0.2550292 l -0.17427,-0.4760546 q 0.905354,-0.4633033 1.683194,-0.4633033 1.513173,0 1.513173,1.6024341 v 1.9042187 q 0,0.57806645 0.110513,1.0286182 z m -0.773589,-1.3134009 v -0.8033422 q -0.896853,0.080759 -1.232641,0.1530175 -0.331538,0.068008 -0.578067,0.2592798 -0.242278,0.191272 -0.242278,0.5185596 0,0.29753416 0.208274,0.48030515 0.208274,0.182771 0.531311,0.182771 0.352791,0 0.701331,-0.20827393 0.34854,-0.21252441 0.61207,-0.58231692 z" + id="path1472" /> - - + d="M 71.901329,0.88835204 71.642049,1.253894 Q 70.69419,0.53556152 70.196883,-0.41654785 69.699576,-1.3686572 69.699576,-2.4270288 q 0,-1.0668725 0.493056,-2.0104809 0.493057,-0.9478589 1.449417,-1.6661914 l 0.25928,0.365542 q -0.77784,0.69708 -1.122129,1.4621679 -0.340039,0.7608374 -0.340039,1.8404614 0,1.1178784 0.35279,1.88296633 0.357041,0.76083739 1.109378,1.44091551 z" + id="path1474" /> + d="m 74.446112,-6.1037011 q 0.95211,0.7183325 1.445166,1.6661914 0.493057,0.9436084 0.493057,2.0104809 0,1.0583716 -0.497307,2.01048095 -0.493057,0.95210937 -1.440916,1.67044185 l -0.26353,-0.36554196 q 0.777839,-0.68857909 1.117878,-1.46216795 0.34429,-0.77783939 0.34429,-1.86171389 0,-1.1178784 -0.35279,-1.8702148 -0.352791,-0.7523364 -1.109378,-1.4324145 z" + id="path1476" /> + + + aria-label="3" + transform="matrix(1,0,0,-1,387.85,540.602)" + id="text12469" + style="font-size:5.302px;font-family:'Liberation Sans';-inkscape-font-specification:LiberationSans"> + d="m 2.7157217,-1.0070693 q 0,0.50482906 -0.3210195,0.78183785 -0.3210196,0.27700879 -0.916459,0.27700879 -0.55401761,0 -0.88539261,-0.24853125 -0.32878613,-0.25112012 -0.39091895,-0.74041602 l 0.4815293,-0.0440107 q 0.0931992,0.6472168 0.79478226,0.6472168 0.3520859,0 0.5514287,-0.1734541 0.2019316,-0.17345411 0.2019316,-0.51518453 0,-0.2977198 -0.2304091,-0.4634073 Q 1.773374,-1.6542861 1.3410332,-1.6542861 H 1.0769688 v -0.4038633 h 0.2537089 q 0.3831524,0 0.5928506,-0.1656875 0.2122871,-0.1682764 0.2122871,-0.4634073 0,-0.292542 -0.1734541,-0.4608183 -0.1708652,-0.1708653 -0.5100068,-0.1708653 -0.3080752,0 -0.49965137,0.1579209 -0.1889873,0.1579209 -0.22005371,0.4452852 L 0.26406446,-2.7519658 Q 0.3158418,-3.1998399 0.63427247,-3.45096 0.955292,-3.7020801 1.4575322,-3.7020801 q 0.5488399,0 0.8517374,0.2562978 0.3054863,0.253709 0.3054863,0.7093497 0,0.349497 -0.1967539,0.5695507 -0.1941651,0.2174649 -0.5669619,0.2951309 v 0.010355 q 0.409041,0.044011 0.6368613,0.2744199 0.2278203,0.2304092 0.2278203,0.5799063 z" + id="path1445" /> + + + aria-label="Alpha_diversity_graph()" + transform="matrix(1,0,0,-1,309.55,527.408)" + id="text12475" + style="font-size:8.705px;font-family:'Andale Mono';-inkscape-font-specification:AndaleMono"> - - + d="M 4.9985742,0 H 4.2674902 L 3.604414,-2.0997412 H 1.636438 L 0.96486083,0 h -0.722583 L 2.2017529,-5.9974389 H 3.0390991 Z M 3.4046411,-2.707561 2.6183008,-5.1898461 1.8362109,-2.707561 Z" + id="path1398" /> - - + d="M 9.22696,0 H 7.416252 V -5.423623 H 6.2601192 v -0.5738159 h 1.8192089 v 5.42362299 H 9.22696 Z" + id="path1400" /> - - + d="m 12.005521,-3.8551928 q 0.221025,-0.3060352 0.595068,-0.4930567 0.378294,-0.1870215 0.794842,-0.1870215 0.765087,0 1.198637,0.6333228 0.437801,0.6290723 0.437801,1.6406885 0,1.0201171 -0.459053,1.70019525 -0.454802,0.67582763 -1.228391,0.67582763 -0.412298,0 -0.773589,-0.20402343 -0.357041,-0.20827393 -0.565315,-0.54831299 V 1.7512012 h -0.663076 v -6.18021 h 0.663076 z m 0,0.6588256 v 1.8404615 q 0.187021,0.37404292 0.505808,0.62482172 0.318787,0.25077881 0.658826,0.25077881 0.535561,0 0.850097,-0.50155761 0.318787,-0.50155762 0.318787,-1.24539302 0,-0.7650879 -0.301785,-1.2496436 -0.301784,-0.4845556 -0.841596,-0.4845556 -0.701331,0 -1.190137,0.7650878 z" + id="path1402" /> - - + d="m 19.978587,0 h -0.663076 v -2.8393261 q 0,-0.5908179 -0.191272,-0.8543482 -0.187021,-0.2677807 -0.590818,-0.2677807 -0.607819,0 -1.3049,0.7565869 V 0 h -0.663076 v -5.9974389 h 0.663076 v 2.2187549 q 0.714083,-0.756587 1.504673,-0.756587 1.245393,0 1.245393,1.5046729 z" + id="path1404" /> - - + d="m 25.3121,0 h -0.658826 q -0.08076,-0.26778076 -0.08076,-0.71408202 -0.565315,0.8288452 -1.538677,0.8288452 -0.493057,0 -0.87135,-0.34854003 -0.374043,-0.35279053 -0.374043,-0.90535395 0,-0.3272876 0.131765,-0.5780665 0.131765,-0.2507788 0.386794,-0.4207983 0.25503,-0.17427 0.620572,-0.2720312 0.365542,-0.1020118 0.867099,-0.1402661 l 0.743836,-0.059507 v -0.2125244 q 0,-1.1391308 -1.062622,-1.1391308 -0.250779,0 -0.637574,0.1105127 -0.382543,0.1062622 -0.658825,0.2550292 l -0.17427,-0.4760546 q 0.905354,-0.4633033 1.683193,-0.4633033 1.513174,0 1.513174,1.6024341 v 1.9042187 q 0,0.57806645 0.110513,1.0286182 z m -0.773589,-1.3134009 v -0.8033422 q -0.896853,0.080759 -1.232642,0.1530175 -0.331538,0.068008 -0.578066,0.2592798 -0.242278,0.191272 -0.242278,0.5185596 0,0.29753416 0.208274,0.48030515 0.208274,0.182771 0.531311,0.182771 0.35279,0 0.70133,-0.20827393 0.348541,-0.21252441 0.612071,-0.58231692 z" + id="path1406" /> - - + d="m 31.304029,1.8957178 h -5.22385 v -0.556814 h 5.22385 z" + id="path1408" /> - - + d="M 35.613176,0 H 34.9501 v -0.63757324 q -0.204024,0.3272876 -0.586568,0.53981201 -0.378293,0.21252441 -0.799092,0.21252441 -0.760837,0 -1.202888,-0.67582763 -0.442051,-0.68007815 -0.442051,-1.72144775 0,-0.9733618 0.459053,-1.610935 0.463303,-0.6418238 1.224141,-0.6418238 0.837346,0 1.347405,0.6800782 v -2.1422461 h 0.663076 z M 34.9501,-1.3559057 v -1.8404615 q -0.476055,-0.7650878 -1.147632,-0.7650878 -0.548313,0 -0.8671,0.4888061 -0.318786,0.4845557 -0.318786,1.2283911 0,0.7650879 0.297534,1.2666455 0.301784,0.49730713 0.824594,0.49730713 0.250779,0 0.505809,-0.13601563 0.255029,-0.13601562 0.480305,-0.4080469 0.225276,-0.2720312 0.225276,-0.331538 z" + id="path1410" /> - - + d="m 39.425013,-6.1037011 q 0.187022,0 0.318787,0.1360156 0.131765,0.1317651 0.131765,0.3187866 0,0.1955225 -0.131765,0.3272876 -0.127515,0.1317652 -0.318787,0.1317652 -0.17427,0 -0.310285,-0.1360157 -0.131766,-0.1402661 -0.131766,-0.3230371 0,-0.182771 0.131766,-0.3187866 0.136015,-0.1360156 0.310285,-0.1360156 z M 39.74805,0 h -0.663076 v -3.8551928 h -1.3049 v -0.573816 h 1.967976 z" + id="path1412" /> + + + + + + + d="M 77.56172,-4.4290088 75.882777,0 q -0.365542,0.9776123 -0.726833,1.3644067 -0.357041,0.3867945 -0.816094,0.3867945 -0.408047,0 -0.807593,-0.1487671 L 73.64277,1.071123 q 0.323037,0.1020118 0.578066,0.1020118 0.357041,0 0.586568,-0.27628178 0.229526,-0.27628174 0.463303,-0.905354 L 73.608766,-4.4290088 h 0.722583 l 1.253894,3.53215578 1.253894,-3.53215578 z" + id="path1426" /> + + + + + + + + + + + aria-label="4" + transform="matrix(1,0,0,-1,429.602,530.416)" + id="text12481" + style="font-size:5.302px;font-family:'Liberation Sans';-inkscape-font-specification:LiberationSans"> + d="M 2.280792,-0.82584864 V 0 H 1.8406846 V -0.82584864 H 0.12167676 V -1.18829 L 1.7914961,-3.6477139 H 2.280792 v 2.4542461 h 0.5125957 v 0.36761916 z M 1.8406846,-3.1221739 q -0.00518,0.015533 -0.072488,0.13721 -0.067311,0.1216768 -0.1009658,0.1708652 l -0.93458108,1.3772774 -0.13979883,0.1915762 -0.0414219,0.051777 H 1.8406846 Z" + id="path1395" /> + + + aria-label="mp_plot_venn()" + transform="matrix(1,0,0,-1,309.55,515.817)" + id="text12487" + style="font-size:8.705px;font-family:'Andale Mono';-inkscape-font-specification:AndaleMono"> + + + + + d="m 24.87855,0 h -1.810708 v -5.423623 h -1.156133 v -0.5738159 h 1.819209 v 5.42362299 h 1.147632 z" + id="path1374" /> + + + + + + + + + + + + aria-label="3" + transform="matrix(1,0,0,-1,382.622,518.825)" + id="text12493" + style="font-size:5.302px;font-family:'Andale Mono';-inkscape-font-specification:AndaleMono"> + d="m 1.8173848,-1.9623613 q 0.3339639,0.093199 0.5358955,0.3417304 0.2019316,0.2459424 0.2019316,0.5540176 0,0.48152931 -0.3753857,0.81031545 -0.3753858,0.32619726 -0.8853926,0.32619726 -0.43492969,0 -0.77924903,-0.19157617 l 0.0828438,-0.34949707 q 0.35985254,0.16827637 0.71193847,0.16827637 0.331375,0 0.5643731,-0.20452051 0.2355869,-0.20710938 0.2355869,-0.53071783 0,-0.3184306 -0.2511201,-0.5177734 Q 1.6076865,-1.755252 1.1934678,-1.755252 H 1.0821465 v -0.349497 h 0.031066 q 0.3986856,0 0.6575723,-0.1863985 0.2588867,-0.1889873 0.2588867,-0.507418 0,-0.2588867 -0.1863984,-0.4038632 -0.1863985,-0.1475655 -0.5125958,-0.1475655 -0.2821865,0 -0.63168355,0.1527432 L 0.64203907,-3.5622813 Q 0.99412501,-3.722791 1.3513887,-3.722791 q 0.4892959,0 0.8051377,0.2588867 0.3184307,0.2562978 0.3184307,0.6601611 0,0.2795977 -0.1941651,0.5229512 -0.1915762,0.2407646 -0.4634072,0.3028975 z" + id="path1363" /> + + + aria-label="dist_permanova()" + transform="matrix(1,0,0,-1,309.55,480.625)" + id="text12499" + style="font-size:8.705px;font-family:'Andale Mono';-inkscape-font-specification:AndaleMono"> + + + + d="m 20.021092,-0.19977295 q -0.667326,0.30603516 -1.313401,0.30603516 -1.185886,0 -1.185886,-1.25389401 v -2.707561 h -0.850097 v -0.573816 h 0.850097 v -1.2113891 h 0.646074 v 1.2113891 h 1.504673 v 0.573816 h -1.504673 v 2.533291 q 0,0.40379634 0.178521,0.62907222 0.17852,0.22102538 0.484556,0.22102538 0.544062,0 1.075373,-0.24227782 z" + id="path1336" /> + + + + + + + + + + + + + + + aria-label="2" + transform="matrix(1,0,0,-1,393.078,483.634)" + id="text12505" + style="font-size:5.302px;font-family:'Andale Mono';-inkscape-font-specification:AndaleMono"> + d="M 2.5396787,0 H 0.53071778 v -0.3080752 q 0.76371582,-0.8517373 0.99153612,-1.1416904 0.2278203,-0.2899532 0.370208,-0.6083838 0.1423877,-0.3184307 0.1423877,-0.6342725 0,-0.3054863 -0.1863984,-0.4815293 -0.1838096,-0.176043 -0.5177735,-0.176043 -0.2562978,0 -0.68863863,0.1579209 l -0.059544,-0.3650302 Q 0.97341407,-3.722791 1.4005772,-3.722791 q 0.4892959,0 0.7870156,0.2770087 0.3003086,0.27442 0.3003086,0.7352383 0,0.3287862 -0.155332,0.6523946 -0.1527432,0.3236084 -0.3935079,0.6213281 -0.2407646,0.2977197 -0.9371699,1.06661329 h 1.5377871 z" + id="path1327" /> + + + aria-label="Mp_adonis()" + transform="matrix(1,0,0,-1,309.55,470.366)" + id="text12511" + style="font-size:8.705px;font-family:'Andale Mono';-inkscape-font-specification:AndaleMono"> + d="M 4.5437719,0 H 3.8721948 v -5.1430908 l -0.905354,2.4610327 H 2.3080151 L 1.4026611,-5.1430908 V 0 H 0.73108398 V -5.9974389 H 1.636438 l 1.0031152,2.7330639 0.9988647,-2.7330639 h 0.905354 z" + id="path1304" /> + + + + + + + + + + + + + aria-label="3" + transform="matrix(1,0,0,-1,366.962,473.374)" + id="text12517" + style="font-size:5.302px;font-family:'Andale Mono';-inkscape-font-specification:AndaleMono"> + d="m 1.8173848,-1.9623613 q 0.3339639,0.093199 0.5358955,0.3417304 0.2019316,0.2459424 0.2019316,0.5540176 0,0.48152931 -0.3753857,0.81031545 -0.3753858,0.32619726 -0.8853926,0.32619726 -0.43492969,0 -0.77924903,-0.19157617 l 0.0828438,-0.34949707 q 0.35985254,0.16827637 0.71193847,0.16827637 0.331375,0 0.5643731,-0.20452051 0.2355869,-0.20710938 0.2355869,-0.53071783 0,-0.3184306 -0.2511201,-0.5177734 Q 1.6076865,-1.755252 1.1934678,-1.755252 H 1.0821465 v -0.349497 h 0.031066 q 0.3986856,0 0.6575723,-0.1863985 0.2588867,-0.1889873 0.2588867,-0.507418 0,-0.2588867 -0.1863984,-0.4038632 -0.1863985,-0.1475655 -0.5125958,-0.1475655 -0.2821865,0 -0.63168355,0.1527432 L 0.64203907,-3.5622813 Q 0.99412501,-3.722791 1.3513887,-3.722791 q 0.4892959,0 0.8051377,0.2588867 0.3184307,0.2562978 0.3184307,0.6601611 0,0.2795977 -0.1941651,0.5229512 -0.1915762,0.2407646 -0.4634072,0.3028975 z" + id="path1301" /> + + + aria-label="tsne_phyloseq()" + transform="matrix(1,0,0,-1,309.55,458.726)" + id="text12523" + style="font-size:8.705px;font-family:'Andale Mono';-inkscape-font-specification:AndaleMono"> + + + d="m 14.755587,0 h -0.663076 v -2.8393261 q 0,-0.5908179 -0.191272,-0.8543482 -0.187022,-0.2677807 -0.590818,-0.2677807 -0.60782,0 -1.3049,0.7565869 V 0 h -0.663076 v -4.4290088 h 0.663076 v 0.6503248 q 0.714082,-0.756587 1.504673,-0.756587 1.245393,0 1.245393,1.5046729 z" + id="path1274" /> + + + + + + + + + + + + + + + aria-label="4" + transform="matrix(1,0,0,-1,387.85,461.734)" + id="text12529" + style="font-size:5.302px;font-family:'Andale Mono';-inkscape-font-specification:AndaleMono"> + d="M 2.7778545,-0.84397071 H 2.3273916 V 0 H 1.9028174 V -0.84397071 H 0.31325293 V -1.1675791 L 1.755252,-3.6528916 h 0.5721396 v 2.4387129 H 2.7778545 Z M 1.9028174,-1.2141787 v -2.0193164 l -1.15981251,2.0193164 z" + id="path1267" /> + + + aria-label="PlotAbundance()" + transform="matrix(1,0,0,-1,309.55,446.642)" + id="text12535" + style="font-size:8.705px;font-family:'Andale Mono';-inkscape-font-specification:AndaleMono"> + d="m 1.088125,-5.9974389 h 1.5216748 q 0.8628491,0 1.3814087,0.4335498 0.5185595,0.4335498 0.5185595,1.1943872 0,0.7650879 -0.5185595,1.2241406 -0.5143091,0.4548022 -1.3516553,0.4548022 H 1.7852051 V 0 H 1.088125 Z m 0.6970801,2.69906 H 2.541792 q 1.2283911,0 1.2283911,-1.0286181 0,-0.4760547 -0.3357886,-0.7693384 Q 3.1028564,-5.3896191 2.5757959,-5.3896191 H 1.7852051 Z" + id="path1236" /> + + + + + + + + + + + + + + + + + aria-label="1" + transform="matrix(1,0,0,-1,387.85,449.65)" + id="text12541" + style="font-size:5.302px;font-family:'Andale Mono';-inkscape-font-specification:AndaleMono"> + d="M 2.6354668,0 H 0.71452735 V -0.37020801 H 1.4885986 V -3.2076065 L 0.75853809,-2.8425762 V -3.2671504 L 1.5481426,-3.6736026 h 0.3650303 v 3.30339459 h 0.7222939 z" + id="path1233" /> + + + aria-label="comp_barplot()" + transform="matrix(1,0,0,-1,309.55,436.382)" + id="text12547" + style="font-size:8.705px;font-family:'Andale Mono';-inkscape-font-specification:AndaleMono"> + + + + + + + d="m 35.74069,0 h -0.658825 q -0.08076,-0.26778076 -0.08076,-0.71408202 -0.565314,0.8288452 -1.538676,0.8288452 -0.493057,0 -0.87135,-0.34854003 -0.374043,-0.35279053 -0.374043,-0.90535395 0,-0.3272876 0.131765,-0.5780665 0.131765,-0.2507788 0.386794,-0.4207983 0.25503,-0.17427 0.620572,-0.2720312 0.365542,-0.1020118 0.867099,-0.1402661 l 0.743836,-0.059507 v -0.2125244 q 0,-1.1391308 -1.062623,-1.1391308 -0.250778,0 -0.637573,0.1105127 -0.382544,0.1062622 -0.658825,0.2550292 l -0.17427,-0.4760546 q 0.905354,-0.4633033 1.683193,-0.4633033 1.513174,0 1.513174,1.6024341 v 1.9042187 q 0,0.57806645 0.110512,1.0286182 z m -0.773588,-1.3134009 v -0.8033422 q -0.896853,0.080759 -1.232642,0.1530175 -0.331538,0.068008 -0.578066,0.2592798 -0.242278,0.191272 -0.242278,0.5185596 0,0.29753416 0.208274,0.48030515 0.208274,0.182771 0.531311,0.182771 0.35279,0 0.70133,-0.20827393 0.34854,-0.21252441 0.612071,-0.58231692 z" + id="path1216" /> + + + + + + + + + + aria-label="2" + transform="matrix(1,0,0,-1,382.622,439.391)" + id="text12553" + style="font-size:5.302px;font-family:'Andale Mono';-inkscape-font-specification:AndaleMono"> + d="M 2.5396787,0 H 0.53071778 v -0.3080752 q 0.76371582,-0.8517373 0.99153612,-1.1416904 0.2278203,-0.2899532 0.370208,-0.6083838 0.1423877,-0.3184307 0.1423877,-0.6342725 0,-0.3054863 -0.1863984,-0.4815293 -0.1838096,-0.176043 -0.5177735,-0.176043 -0.2562978,0 -0.68863863,0.1579209 l -0.059544,-0.3650302 Q 0.97341407,-3.722791 1.4005772,-3.722791 q 0.4892959,0 0.7870156,0.2770087 0.3003086,0.27442 0.3003086,0.7352383 0,0.3287862 -0.155332,0.6523946 -0.1527432,0.3236084 -0.3935079,0.6213281 -0.2407646,0.2977197 -0.9371699,1.06661329 h 1.5377871 z" + id="path1201" /> + + + aria-label="mp_plot_abundance()" + transform="matrix(1,0,0,-1,309.55,426.123)" + id="text12559" + style="font-size:8.705px;font-family:'Andale Mono';-inkscape-font-specification:AndaleMono"> + + + + + + + + + + + + + + d="m 72.266871,0 h -0.658826 q -0.08076,-0.26778076 -0.08076,-0.71408202 -0.565315,0.8288452 -1.538677,0.8288452 -0.493057,0 -0.87135,-0.34854003 -0.374043,-0.35279053 -0.374043,-0.90535395 0,-0.3272876 0.131765,-0.5780665 0.131765,-0.2507788 0.386795,-0.4207983 0.255029,-0.17427 0.620571,-0.2720312 0.365542,-0.1020118 0.867099,-0.1402661 l 0.743836,-0.059507 v -0.2125244 q 0,-1.1391308 -1.062622,-1.1391308 -0.250779,0 -0.637573,0.1105127 -0.382544,0.1062622 -0.658826,0.2550292 l -0.17427,-0.4760546 q 0.905354,-0.4633033 1.683193,-0.4633033 1.513174,0 1.513174,1.6024341 v 1.9042187 q 0,0.57806645 0.110513,1.0286182 z m -0.773589,-1.3134009 v -0.8033422 q -0.896853,0.080759 -1.232642,0.1530175 -0.331538,0.068008 -0.578066,0.2592798 -0.242278,0.191272 -0.242278,0.5185596 0,0.29753416 0.208274,0.48030515 0.208274,0.182771 0.531311,0.182771 0.35279,0 0.701331,-0.20827393 0.34854,-0.21252441 0.61207,-0.58231692 z" + id="path1188" /> + + + + + + + + aria-label="3" + transform="matrix(1,0,0,-1,408.738,429.132)" + id="text12565" + style="font-size:5.302px;font-family:'Andale Mono';-inkscape-font-specification:AndaleMono"> + d="m 1.8173848,-1.9623613 q 0.3339639,0.093199 0.5358955,0.3417304 0.2019316,0.2459424 0.2019316,0.5540176 0,0.48152931 -0.3753857,0.81031545 -0.3753858,0.32619726 -0.8853926,0.32619726 -0.43492969,0 -0.77924903,-0.19157617 l 0.0828438,-0.34949707 q 0.35985254,0.16827637 0.71193847,0.16827637 0.331375,0 0.5643731,-0.20452051 0.2355869,-0.20710938 0.2355869,-0.53071783 0,-0.3184306 -0.2511201,-0.5177734 Q 1.6076865,-1.755252 1.1934678,-1.755252 H 1.0821465 v -0.349497 h 0.031066 q 0.3986856,0 0.6575723,-0.1863985 0.2588867,-0.1889873 0.2588867,-0.507418 0,-0.2588867 -0.1863984,-0.4038632 -0.1863985,-0.1475655 -0.5125958,-0.1475655 -0.2821865,0 -0.63168355,0.1527432 L 0.64203907,-3.5622813 Q 0.99412501,-3.722791 1.3513887,-3.722791 q 0.4892959,0 0.8051377,0.2588867 0.3184307,0.2562978 0.3184307,0.6601611 0,0.2795977 -0.1941651,0.5229512 -0.1915762,0.2407646 -0.4634072,0.3028975 z" + id="path1159" /> + + + aria-label="Phylogeny_profile()" + transform="matrix(1,0,0,-1,309.55,415.864)" + id="text12571" + style="font-size:8.705px;font-family:'Andale Mono';-inkscape-font-specification:AndaleMono"> + + + + + + + + d="m 40.853177,0 h -0.663076 v -2.8393261 q 0,-0.5908179 -0.191272,-0.8543482 -0.187021,-0.2677807 -0.590818,-0.2677807 -0.60782,0 -1.3049,0.7565869 V 0 h -0.663076 v -4.4290088 h 0.663076 v 0.6503248 q 0.714082,-0.756587 1.504673,-0.756587 1.245393,0 1.245393,1.5046729 z" + id="path1134" /> + + + + + + + + + + + + + + aria-label="4" + transform="matrix(1,0,0,-1,408.738,418.873)" + id="text12577" + style="font-size:5.302px;font-family:'Andale Mono';-inkscape-font-specification:AndaleMono"> + d="M 2.7778545,-0.84397071 H 2.3273916 V 0 H 1.9028174 V -0.84397071 H 0.31325293 V -1.1675791 L 1.755252,-3.6528916 h 0.5721396 v 2.4387129 H 2.7778545 Z M 1.9028174,-1.2141787 v -2.0193164 l -1.15981251,2.0193164 z" + id="path1117" /> + + + - MiscMetabar + aria-label="Mp_diff_analysis()" + transform="matrix(1,0,0,-1,305.21,368.465)" + id="text12585" + style="font-size:8.705px;font-family:'Andale Mono';-inkscape-font-specification:AndaleMono"> + + + + + + + + + + + + + + + + + + + + - Other packages + aria-label="3" + transform="matrix(1,0,0,-1,399.17,371.474)" + id="text12591" + style="font-size:5.302px;font-family:'Andale Mono';-inkscape-font-specification:AndaleMono"> + - - 1. Mia — 2. microViz — 3.MicrobiotaProcess — 4. Phylosmith - - - Conversion to physeq - - - Conversion from physeq - - - Describe - - - summary_plot_pq() - - - krona() - - - sankey_pq() - - - accu_plot() - - - SRS_curve_pq() - - - clean_pq() - - - filter_asv_blast() - - - asv2otu() - - - lulu_pq() - - - E - x - p - l - o - r - e - - - Alpha-diversity - - - hill_pq() - - - Beta-diversity - - - ggvenn_pq() - - - upset_pq() - - - graph_test_pq() - - - adonis_pq() - - - plot_tsne_pq() - - - plot_tax_pq() - - - circle_pq() - - - amplicon::tax_circlize() - - - Compare 2 modalities - - - biplot_pq() - - - compare_pairs_pq() - - - Differential abundance - - - plot_deseq2_pq() - - - Taxonomy - - - blast_pq() - - - heat_tree_pq() - - - tax_datatable() - - - multitax_bar_pq() - - - treemap_pq() - - - Reproduce - - - write_pq() - - - read_pq() - - - list_fastq_files() - - - track_wkflow() - - - track_wkflow_samples() - - - MakeTreeSEFromPhyloseq() - - - 1 - - - as.MPSE() - - - 3 - - - MakePhyloseqFromTreeSE() - - - 1 - - - as.phyloseq() - - - 3 - - - mp_plot_rarecurve() - - - 3 - - - Transform - - - See also table 2 - - - EstimateDiversity() - - - 1 - - - mp_plot_alpha() - - - 3 - - - Alpha_diversity_graph() - - - 4 - - - mp_plot_venn() - - - 3 - - - dist_permanova() - - - 2 - - - Mp_adonis() - - - 3 - - - tsne_phyloseq() - - - 4 - - - PlotAbundance() - - - 1 - - - comp_barplot() - - - 2 - - - mp_plot_abundance() - - - 3 - - - Phylogeny_profile() - - - 4 - - - - Mp_diff_analysis() - - - 3 - - A - C - B - D - E - F - G - H - I - - - Fig.2 + + + + + + + + + + + + d="m 700.08388,363.98019 q 0,0.60146 -0.12856,1.14781 -0.12396,0.54177 -0.40403,0.95498 -0.27547,0.40862 -0.71623,0.65196 -0.43617,0.24333 -1.05598,0.24333 h -1.94669 v -5.99156 h 1.94669 q 0.61063,0 1.0468,0.24793 0.44076,0.24333 0.71623,0.65195 0.28007,0.40862 0.40862,0.95039 0.13315,0.54176 0.13315,1.14321 z m -0.95039,0 q 0,-1.03761 -0.35352,-1.58397 -0.35353,-0.55095 -1.00089,-0.55095 h -0.9963 v 4.27903 h 0.9963 q 0.64736,0 1.00089,-0.56013 0.35352,-0.56013 0.35352,-1.58398 z" + id="path1065" /> + + + + + + + + + d="m 700.12061,363.99856 q 0,0.61063 -0.12397,1.16617 -0.11937,0.55554 -0.39943,0.98253 -0.27548,0.42698 -0.71624,0.68409 -0.43616,0.25252 -1.06516,0.25252 -0.629,0 -1.06517,-0.25711 -0.43617,-0.2617 -0.71623,-0.68868 -0.27548,-0.42699 -0.39944,-0.98712 -0.11937,-0.56013 -0.11937,-1.16158 0,-0.60145 0.11937,-1.16159 0.12396,-0.56013 0.39944,-0.9917 0.28006,-0.43158 0.71623,-0.68869 0.43617,-0.2617 1.06517,-0.2617 0.17905,0 0.36729,0.0505 0.18825,0.0505 0.35812,0.1561 0.16988,0.101 0.29843,0.25252 0.13315,0.15151 0.18824,0.34893 v -0.70705 h 0.85856 v 2.12574 h -0.85856 q 0,-0.28006 -0.0872,-0.52799 -0.0872,-0.25252 -0.24793,-0.44076 -0.16069,-0.18824 -0.38566,-0.29384 -0.22497,-0.11019 -0.49126,-0.11019 -0.40403,0 -0.66114,0.20202 -0.25711,0.20201 -0.41321,0.5234 -0.1561,0.32138 -0.22038,0.72082 -0.0597,0.39944 -0.0597,0.80347 0,0.40403 0.0597,0.80346 0.0643,0.39944 0.21579,0.72083 0.15151,0.31679 0.41321,0.51422 0.2617,0.19742 0.66573,0.19742 0.58308,0 0.9412,-0.37189 0.35812,-0.37189 0.49126,-1.1524 h -1.26259 v -0.85397 h 2.13493 z" + id="path1056" /> + + + + + + d="m 699.19777,366.97827 h -2.87412 v -0.85397 h 0.9458 v -4.27903 h -0.9458 v -0.85856 h 2.87412 v 0.85856 h -0.97794 v 4.27903 h 0.97794 z" + id="path1050" /> + + + + d="m 699.66148,361.84527 h -2.8787 v 1.65285 h 2.24511 v 0.85856 h -2.24511 v 2.62159 h -0.95039 v -5.99156 h 3.82909 z" + id="path1038" /> + d="m 703.45843,362.1437 h -1.15699 v -1.15699 h 1.15699 z m 0.87234,4.83457 h -2.87411 v -0.85397 h 0.94579 v -2.5665 h -0.94579 v -0.85856 h 1.89618 v 3.42506 h 0.97793 z" + id="path1040" /> + d="m 709.92749,366.93236 q 0,0.44076 -0.15152,0.7851 -0.15151,0.34434 -0.42698,0.58309 -0.27088,0.23874 -0.64277,0.3627 -0.3673,0.12856 -0.82183,0.12856 -1.11567,0 -1.90537,-0.67491 l 0.44994,-0.7346 q 0.65655,0.56472 1.45543,0.56472 0.49126,0 0.78969,-0.24333 0.30302,-0.23875 0.30302,-0.75297 v -0.45912 q -0.29384,0.25252 -0.56472,0.37648 -0.27089,0.11937 -0.629,0.11937 -0.41321,0 -0.76674,-0.17446 -0.35352,-0.17447 -0.61063,-0.4729 -0.25252,-0.30302 -0.39944,-0.70246 -0.14233,-0.39944 -0.14233,-0.84938 0,-0.44994 0.14233,-0.84938 0.14692,-0.40403 0.39944,-0.69786 0.25711,-0.29843 0.61063,-0.46831 0.35353,-0.17447 0.76674,-0.17447 0.35811,0 0.63818,0.12397 0.28007,0.11937 0.55554,0.3627 v -0.38566 h 0.95039 z m -0.95039,-3.09449 q -0.16988,-0.18824 -0.44076,-0.28466 -0.26629,-0.10101 -0.51881,-0.10101 -0.53717,0 -0.87233,0.37648 -0.33057,0.37649 -0.33057,0.95957 0,0.28925 0.0872,0.53718 0.0918,0.24333 0.24793,0.42239 0.16069,0.17906 0.38107,0.28466 0.22497,0.101 0.48667,0.101 0.25252,0 0.51881,-0.101 0.27088,-0.1056 0.44076,-0.29384 z" + id="path1042" /> + d="m 713.72444,366.97827 h -1.15699 v -1.15699 h 1.15699 z" + id="path1044" /> + d="m 720.2945,362.62578 q 0,0.42239 -0.22498,0.86315 -0.22497,0.44076 -0.61981,0.83561 l -1.87323,1.79976 h 1.75845 v -0.82183 h 0.85856 v 1.6758 h -3.85664 v -0.89529 l 2.41499,-2.30939 q 0.3122,-0.32139 0.44994,-0.60145 0.14233,-0.28466 0.14233,-0.54636 0,-0.23415 -0.0918,-0.40403 -0.0872,-0.16987 -0.22956,-0.27547 -0.13773,-0.11019 -0.31679,-0.1561 -0.17906,-0.0505 -0.35812,-0.0505 -0.56472,0 -0.8907,0.33057 -0.32138,0.33057 -0.32138,0.97793 h -0.8907 q 0,-1.01466 0.53717,-1.58856 0.54177,-0.57391 1.56561,-0.57391 0.38567,0 0.73919,0.11478 0.35353,0.11019 0.61982,0.32598 0.27088,0.21579 0.42698,0.54636 0.1607,0.33057 0.1607,0.75296 z" + id="path1046" /> + + + + + + + + diff --git a/paper/figures_svg/tengeler_MiscMetabar.svg b/paper/figures_svg/tengeler_MiscMetabar.svg index 8489dfff..047636f7 100644 --- a/paper/figures_svg/tengeler_MiscMetabar.svg +++ b/paper/figures_svg/tengeler_MiscMetabar.svg @@ -26,8 +26,8 @@ inkscape:document-units="pt" showgrid="false" inkscape:zoom="0.32" - inkscape:cx="842.1875" - inkscape:cy="907.8125" + inkscape:cx="753.125" + inkscape:cy="970.3125" inkscape:window-width="1280" inkscape:window-height="995" inkscape:window-x="1920" @@ -12250,138 +12250,98 @@ style="font-size:8.8px;font-family:Arial" textLength="17.200001" lengthAdjust="spacingAndGlyphs" - id="text29719">A39AA39BCDEFGHI + rdf:about="" /> From b6b69352ac6fcf9c6c918e60a88ad9f39151fca0 Mon Sep 17 00:00:00 2001 From: Adrien Taudiere Date: Tue, 12 Dec 2023 10:08:10 +0100 Subject: [PATCH 3/7] better images for publication --- .../tengeler_MiscMetabar_editable.svg | 12387 ++++++++++++++++ 1 file changed, 12387 insertions(+) create mode 100644 paper/figures_svg/tengeler_MiscMetabar_editable.svg diff --git a/paper/figures_svg/tengeler_MiscMetabar_editable.svg b/paper/figures_svg/tengeler_MiscMetabar_editable.svg new file mode 100644 index 00000000..07df5188 --- /dev/null +++ b/paper/figures_svg/tengeler_MiscMetabar_editable.svg @@ -0,0 +1,12387 @@ + +151 taxa 485 932 sequences 1 534 occurrences6 taxonomic levels4 variables 27 samplesSequences length: No refseq slot@otu_table@tax_table@sam_data@refseqTaxa(OTUs, ASVs, ...)SamplesMin nb seq per sample (A291772Nb samples with less than 500 seq : 0Min nb seq per taxa: 173 (1 ASV)Min seq length: No refseq slotMax nb seq 1 taxa in 1 sample: 17722Max nb of sample for one taxa (1726472): 27Nb of taxa present in 1 sample only: 0ADHDControl304050607080Richness (Hill 0)patient_status1020Shannon (Hill 1)4812Simpson (Hill 2)Hill Number 0 Control-ADHDHill Number 1 Control-ADHDHill Number 2 Control-ADHD-10-50510Differences in mean levels (value and confidence intervals at 95%)Tuckey HSD testing for differences in mean Hill numbers531141745312631121341434212111102040Intersection size050100Set sizeControl_Cohort_1ADHD_Cohort_3Control_Cohort_3ADHD_Cohort_2Control_Cohort_2ADHD_Cohort_1patient_status_vs_cohortBacteriaFirmicutesVerrucomicrobiaBacteroidetesProteobacteriaCyanobacteriaClostridiaErysipelotrichiaVerrucomicrobiaeBacteroidiaGammaproteobacteriaMelainabacteriaClostridialesErysipelotrichalesVerrucomicrobialesBacteroidalesOceanospirillalesEnterobacterialesGastranaerophilalesRuminococcaceaeErysipelotrichaceaeLachnospiraceaeVerrucomicrobiaceaeClostridiaceae_1PorphyromonadaceaeBacteroidales_S24-7_groupBacteroidaceaePrevotellaceaeRikenellaceaeHalomonadaceaeEnterobacteriaceaeChristensenellaceaeEubacteriaceae[Eubacterium]_coprostanoligenes_group[Clostridium]_innocuum_groupDielmaEpulopisciumHoldemaniaAkkermansiaErysipelatoclostridiumClostridium_sensu_stricto_1Parabacteroidesuncultured_bacteriumunculturedCoprobacterBacteroidesParaprevotellaBarnesiellaOdoribacterAlistipesHalomonasEscherichia-ShigellaCoprococcus_2FusicatenibacterLachnoclostridium[Ruminococcus]_gnavus_groupHungatellaunculturedEisenbergiella[Eubacterium]_rectale_group[Ruminococcus]_gauvreauii_groupRoseburiaAnaerostipes[Eubacterium]_xylanophilum_group[Eubacterium]_fissicatena_groupCatabacterLachnospiraceae_ND3007_groupRuminococcaceae_UCG-014ButyricicoccusRuminococcaceae_UCG-004unculturedFlavonifractorRuminiclostridium_9AnaerotruncusRuminococcus_2FaecalibacteriumRuminococcus_1SubdoligranulumRuminiclostridium_5Ruminococcaceae_UCG-013EubacteriumBlautia 1.0 14.0 30.4 51.1 77.1110.0151.0 182 16200 58300126000220000340000486000..2..1NodesCohort_1 (10 sam.)Cohort_2 (10 sam.)Cohort_3 (7 sam.)0(0%)0(0%)0(0%)24(16%)2(1%)8(5%)117(77%)-20-100102030BacteroidesFaecalibacteriumParaprevotellaHungatellaRuminococcaceae_UCG-013Ruminococcaceae_UCG-014ParabacteroidesunculturedCatabacter[Ruminococcus]_gauvreauii_groupBlautiataxlog2FoldChangecol_taxBacteroidetesFirmicutesChange in abundance for patient_status (top:ADHD vs down:Control)ADHDControlBacteroidetesCyanobacteriaFirmicutesProteobacteriaVerrucomicrobiaBacteroidiaMelainabacteriaClostridiaErysipelotrichiaGammaproteobacteriaVerrucomicrobiae012345012345BacteroidalesGastranaerophilalesClostridialesErysipelotrichalesEnterobacterialesOceanospirillalesVerrucomicrobialesAbundanceLVL3Control (14 samples)Control (14 samples)ADHD (13 samples)ADHD (13 samples)6625255741276002356822263199871707614726129481034681787192560250404534447142964229387938753743364433623226318731443116304530402693265524872466239223072230195218631732169616631626130711701079107910689388607466465334341726471517264791726472131726471321726471817264740172647221726476117264714517264781726471901726471917264734172647166172647167172647531726471891726472917264748172647271726472517264747172647241726472172647261726473117264711726470Samples-5.0-2.50.02.55.0Abstats::reorder(OTU, Abundance)modalityADHDControl0255075010000200003000040000Number of sequencesNumber of OTUs (with standard error)factA110A111A12A13A14A15A16A17A18A19A21A210A22A23A24A25A26A27A28A29A33A34A35A36A37A38A39ABCDEFGHI From 34fe842238380264b863bc660f8c9ad4eae49c73 Mon Sep 17 00:00:00 2001 From: Adrien Taudiere Date: Tue, 12 Dec 2023 10:21:33 +0100 Subject: [PATCH 4/7] style: better README --- README.Rmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.Rmd b/README.Rmd index b635656d..2606f93f 100644 --- a/README.Rmd +++ b/README.Rmd @@ -45,7 +45,7 @@ BiocManager. You can install the stable version from [GitHub](https://github.com/) with: -```{r} +```{r, results = 'hide'} if (!require("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } @@ -61,7 +61,7 @@ devtools::install_github("adrientaudiere/MiscMetabar") You can install the development version from [GitHub](https://github.com/) with: -```{r} +```{r, results = 'hide'} if (!require("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } @@ -89,7 +89,7 @@ For developers, I also wrote a vignette describing som [rules of codes](https:// ### Summarize a physeq object -```{r example, message=FALSE} +```{r example} library("MiscMetabar") library("phyloseq") library("magrittr") From 4f54021118b46bd194f192d16bcc90caba4fb1a0 Mon Sep 17 00:00:00 2001 From: Adrien Taudiere Date: Tue, 12 Dec 2023 10:23:16 +0100 Subject: [PATCH 5/7] bugfix: retry github action fix --- .github/workflows/R-CMD-check.yaml | 6 ++++++ .github/workflows/test-coverage.yaml | 6 +++--- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 0f00ebb5..e5cbee3f 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -41,6 +41,12 @@ jobs: with: extra-packages: any::rcmdcheck needs: check + + - name: Install vsearch + run: sudo apt-get install vsearch + + - name: Install blastn + run: sudo apt-get install ncbi-blast+ - uses: r-lib/actions/check-r-package@v2 with: diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 4eeea310..d64ba253 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -34,9 +34,9 @@ jobs: - name: Install mumu run: | git clone https://github.com/frederic-mahe/mumu.git \ - && cd ./mumu/\ - && make\ - && make check\ + && cd ./mumu/ \ + && make \ + && make check \ && sudo make install - name: Test coverage From b2ab9909cf9711025bf667e05c19ff8d218c6e01 Mon Sep 17 00:00:00 2001 From: Adrien Taudiere Date: Tue, 12 Dec 2023 10:27:10 +0100 Subject: [PATCH 6/7] style: better README --- README.md | 206 ++---------------------------------------------------- 1 file changed, 6 insertions(+), 200 deletions(-) diff --git a/README.md b/README.md index 6ccdf213..17090384 100644 --- a/README.md +++ b/README.md @@ -51,117 +51,16 @@ if (!require("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("dada2") -#> 'getOption("repos")' replaces Bioconductor standard repositories, see -#> 'help("repositories", package = "BiocManager")' for details. -#> Replacement repositories: -#> CRAN: https://cloud.r-project.org -#> Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31) #> Warning: package(s) not installed when version(s) same as or greater than current; use #> `force = TRUE` to re-install: 'dada2' -#> Installation paths not writeable, unable to update packages -#> path: /usr/local/lib/R/site-library -#> packages: -#> BH, cpp11, httpgd, Rcpp, rlang, systemfonts -#> Old packages: 'ALDEx2', 'ANCOMBC', 'annotate', 'AnnotationDbi', -#> 'AnnotationHub', 'aricode', 'basilisk', 'basilisk.utils', 'BayesFactor', -#> 'beachmat', 'benchdamic', 'bibliometrix', 'BiocBaseUtils', 'BiocFileCache', -#> 'BiocGenerics', 'BiocNeighbors', 'BiocSingular', 'BiocVersion', 'Biostrings', -#> 'bluster', 'brio', 'bslib', 'Cairo', 'checkmate', 'ComplexHeatmap', 'copula', -#> 'covr', 'crosstalk', 'curl', 'data.table', 'dbplyr', 'dearseq', 'decontam', -#> 'DelayedMatrixStats', 'deldir', 'densvis', 'desc', 'DescTools', 'DESeq2', -#> 'dir.expiry', 'DirichletMultinomial', 'downloadthis', 'dqrng', 'drake', 'DT', -#> 'e1071', 'ecodist', 'edgeR', 'ExperimentHub', 'expm', 'fBasics', 'foreign', -#> 'fstcore', 'gaston', 'gdsfmt', 'genefilter', 'GenomeInfoDb', 'GenomicRanges', -#> 'gert', 'ggiraph', 'ggside', 'ggthemes', 'ggtree', 'ggtreeExtra', 'git2r', -#> 'gmp', 'graphlayouts', 'grImport2', 'gtools', 'haven', 'htmlTable', -#> 'htmlwidgets', 'httpuv', 'insight', 'interactiveDisplayBase', 'interp', -#> 'KEGGREST', 'later', 'lava', 'LEA', 'leaflet', 'leiden', 'limma', 'link2GI', -#> 'lintr', 'lme4', 'lpSolve', 'lpSolveAPI', 'Maaslin2', 'maps', 'markdown', -#> 'MAST', 'Matrix', 'MatrixModels', 'matrixStats', 'mclust', 'mia', -#> 'microbiome', 'microbiomeDataSets', 'MicrobiotaProcess', -#> 'MultiAssayExperiment', 'mvtnorm', 'network', 'nlme', 'NOISeq', 'ordinal', -#> 'osqp', 'pak', 'parameters', 'pcaPP', 'performance', 'plotrix', 'pls', -#> 'pracma', 'processx', 'progress', 'PROJ', 'qgraph', 'qs', 'R.utils', -#> 'rbibutils', 'RcppArmadillo', 'RcppEigen', 'Rdpack', 'report', 'Rfast', -#> 'rgl', 'rhdf5', 'rhdf5filters', 'rJava', 'Rmpfr', 'robustbase', 'rpart', -#> 'RSQLite', 'Rtsne', 's2', 'S4Vectors', 'sass', 'ScaledMatrix', 'scales', -#> 'scater', 'scuttle', 'segmented', 'SeqArray', 'seqinr', 'seriation', -#> 'Seurat', 'SeuratObject', 'shiny', 'shinybusy', 'SingleCellExperiment', -#> 'sna', 'sp', 'SparseArray', 'sparseMatrixStats', 'spatstat.data', -#> 'spatstat.explore', 'spatstat.linnet', 'spatstat.model', 'spatstat.random', -#> 'spatstat.sparse', 'spatstat.utils', 'spdep', 'stringdist', 'stringfish', -#> 'svglite', 'testthat', 'this.path', 'tinytex', 'TMB', 'treeio', -#> 'TreeSummarizedExperiment', 'units', 'V8', 'vroom', 'wesanderson', 'wk', -#> 'Wrench', 'XML', 'xml2', 'zCompositions', 'zinbwave', 'cluster' BiocManager::install("phyloseq") -#> 'getOption("repos")' replaces Bioconductor standard repositories, see -#> 'help("repositories", package = "BiocManager")' for details. -#> Replacement repositories: -#> CRAN: https://cloud.r-project.org -#> Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31) #> Warning: package(s) not installed when version(s) same as or greater than current; use #> `force = TRUE` to re-install: 'phyloseq' -#> Installation paths not writeable, unable to update packages -#> path: /usr/local/lib/R/site-library -#> packages: -#> BH, cpp11, httpgd, Rcpp, rlang, systemfonts -#> Old packages: 'ALDEx2', 'ANCOMBC', 'annotate', 'AnnotationDbi', -#> 'AnnotationHub', 'aricode', 'basilisk', 'basilisk.utils', 'BayesFactor', -#> 'beachmat', 'benchdamic', 'bibliometrix', 'BiocBaseUtils', 'BiocFileCache', -#> 'BiocGenerics', 'BiocNeighbors', 'BiocSingular', 'BiocVersion', 'Biostrings', -#> 'bluster', 'brio', 'bslib', 'Cairo', 'checkmate', 'ComplexHeatmap', 'copula', -#> 'covr', 'crosstalk', 'curl', 'data.table', 'dbplyr', 'dearseq', 'decontam', -#> 'DelayedMatrixStats', 'deldir', 'densvis', 'desc', 'DescTools', 'DESeq2', -#> 'dir.expiry', 'DirichletMultinomial', 'downloadthis', 'dqrng', 'drake', 'DT', -#> 'e1071', 'ecodist', 'edgeR', 'ExperimentHub', 'expm', 'fBasics', 'foreign', -#> 'fstcore', 'gaston', 'gdsfmt', 'genefilter', 'GenomeInfoDb', 'GenomicRanges', -#> 'gert', 'ggiraph', 'ggside', 'ggthemes', 'ggtree', 'ggtreeExtra', 'git2r', -#> 'gmp', 'graphlayouts', 'grImport2', 'gtools', 'haven', 'htmlTable', -#> 'htmlwidgets', 'httpuv', 'insight', 'interactiveDisplayBase', 'interp', -#> 'KEGGREST', 'later', 'lava', 'LEA', 'leaflet', 'leiden', 'limma', 'link2GI', -#> 'lintr', 'lme4', 'lpSolve', 'lpSolveAPI', 'Maaslin2', 'maps', 'markdown', -#> 'MAST', 'Matrix', 'MatrixModels', 'matrixStats', 'mclust', 'mia', -#> 'microbiome', 'microbiomeDataSets', 'MicrobiotaProcess', -#> 'MultiAssayExperiment', 'mvtnorm', 'network', 'nlme', 'NOISeq', 'ordinal', -#> 'osqp', 'pak', 'parameters', 'pcaPP', 'performance', 'plotrix', 'pls', -#> 'pracma', 'processx', 'progress', 'PROJ', 'qgraph', 'qs', 'R.utils', -#> 'rbibutils', 'RcppArmadillo', 'RcppEigen', 'Rdpack', 'report', 'Rfast', -#> 'rgl', 'rhdf5', 'rhdf5filters', 'rJava', 'Rmpfr', 'robustbase', 'rpart', -#> 'RSQLite', 'Rtsne', 's2', 'S4Vectors', 'sass', 'ScaledMatrix', 'scales', -#> 'scater', 'scuttle', 'segmented', 'SeqArray', 'seqinr', 'seriation', -#> 'Seurat', 'SeuratObject', 'shiny', 'shinybusy', 'SingleCellExperiment', -#> 'sna', 'sp', 'SparseArray', 'sparseMatrixStats', 'spatstat.data', -#> 'spatstat.explore', 'spatstat.linnet', 'spatstat.model', 'spatstat.random', -#> 'spatstat.sparse', 'spatstat.utils', 'spdep', 'stringdist', 'stringfish', -#> 'svglite', 'testthat', 'this.path', 'tinytex', 'TMB', 'treeio', -#> 'TreeSummarizedExperiment', 'units', 'V8', 'vroom', 'wesanderson', 'wk', -#> 'Wrench', 'XML', 'xml2', 'zCompositions', 'zinbwave', 'cluster' if (!require("devtools", quietly = TRUE)) { install.packages("devtools") } -#> -#> Attachement du package : 'devtools' -#> L'objet suivant est masqué depuis 'package:BiocManager': -#> -#> install devtools::install_github("adrientaudiere/MiscMetabar") -#> Downloading GitHub repo adrientaudiere/MiscMetabar@HEAD -#> network (1.18.1 -> 1.18.2) [CRAN] -#> scales (1.2.1 -> 1.3.0 ) [CRAN] -#> sna (2.7-1 -> 2.7-2 ) [CRAN] -#> Installing 3 packages: network, scales, sna -#> Installation des packages dans '/tmp/RtmpVdTtbP/temp_libpathd6864a1812db' -#> (car 'lib' n'est pas spécifié) -#> ── R CMD build ───────────────────────────────────────────────────────────────── -#> * checking for file ‘/tmp/RtmpOhxQ8G/remotes3c7b64ea9dfd3/adrientaudiere-MiscMetabar-d599627/DESCRIPTION’ ... OK -#> * preparing ‘MiscMetabar’: -#> * checking DESCRIPTION meta-information ... OK -#> * checking for LF line-endings in source and make files and shell scripts -#> * checking for empty or unneeded directories -#> * building ‘MiscMetabar_0.5.tar.gz’ -#> Installation du package dans '/tmp/RtmpVdTtbP/temp_libpathd6864a1812db' -#> (car 'lib' n'est pas spécifié) ``` You can install the development version from @@ -172,107 +71,16 @@ if (!require("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("dada2") -#> 'getOption("repos")' replaces Bioconductor standard repositories, see -#> 'help("repositories", package = "BiocManager")' for details. -#> Replacement repositories: -#> CRAN: https://cloud.r-project.org -#> Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31) #> Warning: package(s) not installed when version(s) same as or greater than current; use #> `force = TRUE` to re-install: 'dada2' -#> Installation paths not writeable, unable to update packages -#> path: /usr/local/lib/R/site-library -#> packages: -#> BH, cpp11, httpgd, Rcpp, rlang, systemfonts -#> Old packages: 'ALDEx2', 'ANCOMBC', 'annotate', 'AnnotationDbi', -#> 'AnnotationHub', 'aricode', 'basilisk', 'basilisk.utils', 'BayesFactor', -#> 'beachmat', 'benchdamic', 'bibliometrix', 'BiocBaseUtils', 'BiocFileCache', -#> 'BiocGenerics', 'BiocNeighbors', 'BiocSingular', 'BiocVersion', 'Biostrings', -#> 'bluster', 'brio', 'bslib', 'Cairo', 'checkmate', 'ComplexHeatmap', 'copula', -#> 'covr', 'crosstalk', 'curl', 'data.table', 'dbplyr', 'dearseq', 'decontam', -#> 'DelayedMatrixStats', 'deldir', 'densvis', 'desc', 'DescTools', 'DESeq2', -#> 'dir.expiry', 'DirichletMultinomial', 'downloadthis', 'dqrng', 'drake', 'DT', -#> 'e1071', 'ecodist', 'edgeR', 'ExperimentHub', 'expm', 'fBasics', 'foreign', -#> 'fstcore', 'gaston', 'gdsfmt', 'genefilter', 'GenomeInfoDb', 'GenomicRanges', -#> 'gert', 'ggiraph', 'ggside', 'ggthemes', 'ggtree', 'ggtreeExtra', 'git2r', -#> 'gmp', 'graphlayouts', 'grImport2', 'gtools', 'haven', 'htmlTable', -#> 'htmlwidgets', 'httpuv', 'insight', 'interactiveDisplayBase', 'interp', -#> 'KEGGREST', 'later', 'lava', 'LEA', 'leaflet', 'leiden', 'limma', 'link2GI', -#> 'lintr', 'lme4', 'lpSolve', 'lpSolveAPI', 'Maaslin2', 'maps', 'markdown', -#> 'MAST', 'Matrix', 'MatrixModels', 'matrixStats', 'mclust', 'mia', -#> 'microbiome', 'microbiomeDataSets', 'MicrobiotaProcess', -#> 'MultiAssayExperiment', 'mvtnorm', 'network', 'nlme', 'NOISeq', 'ordinal', -#> 'osqp', 'pak', 'parameters', 'pcaPP', 'performance', 'plotrix', 'pls', -#> 'pracma', 'processx', 'progress', 'PROJ', 'qgraph', 'qs', 'R.utils', -#> 'rbibutils', 'RcppArmadillo', 'RcppEigen', 'Rdpack', 'report', 'Rfast', -#> 'rgl', 'rhdf5', 'rhdf5filters', 'rJava', 'Rmpfr', 'robustbase', 'rpart', -#> 'RSQLite', 'Rtsne', 's2', 'S4Vectors', 'sass', 'ScaledMatrix', 'scales', -#> 'scater', 'scuttle', 'segmented', 'SeqArray', 'seqinr', 'seriation', -#> 'Seurat', 'SeuratObject', 'shiny', 'shinybusy', 'SingleCellExperiment', -#> 'sna', 'sp', 'SparseArray', 'sparseMatrixStats', 'spatstat.data', -#> 'spatstat.explore', 'spatstat.linnet', 'spatstat.model', 'spatstat.random', -#> 'spatstat.sparse', 'spatstat.utils', 'spdep', 'stringdist', 'stringfish', -#> 'svglite', 'testthat', 'this.path', 'tinytex', 'TMB', 'treeio', -#> 'TreeSummarizedExperiment', 'units', 'V8', 'vroom', 'wesanderson', 'wk', -#> 'Wrench', 'XML', 'xml2', 'zCompositions', 'zinbwave', 'cluster' BiocManager::install("phyloseq") -#> 'getOption("repos")' replaces Bioconductor standard repositories, see -#> 'help("repositories", package = "BiocManager")' for details. -#> Replacement repositories: -#> CRAN: https://cloud.r-project.org -#> Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31) #> Warning: package(s) not installed when version(s) same as or greater than current; use #> `force = TRUE` to re-install: 'phyloseq' -#> Installation paths not writeable, unable to update packages -#> path: /usr/local/lib/R/site-library -#> packages: -#> BH, cpp11, httpgd, Rcpp, rlang, systemfonts -#> Old packages: 'ALDEx2', 'ANCOMBC', 'annotate', 'AnnotationDbi', -#> 'AnnotationHub', 'aricode', 'basilisk', 'basilisk.utils', 'BayesFactor', -#> 'beachmat', 'benchdamic', 'bibliometrix', 'BiocBaseUtils', 'BiocFileCache', -#> 'BiocGenerics', 'BiocNeighbors', 'BiocSingular', 'BiocVersion', 'Biostrings', -#> 'bluster', 'brio', 'bslib', 'Cairo', 'checkmate', 'ComplexHeatmap', 'copula', -#> 'covr', 'crosstalk', 'curl', 'data.table', 'dbplyr', 'dearseq', 'decontam', -#> 'DelayedMatrixStats', 'deldir', 'densvis', 'desc', 'DescTools', 'DESeq2', -#> 'dir.expiry', 'DirichletMultinomial', 'downloadthis', 'dqrng', 'drake', 'DT', -#> 'e1071', 'ecodist', 'edgeR', 'ExperimentHub', 'expm', 'fBasics', 'foreign', -#> 'fstcore', 'gaston', 'gdsfmt', 'genefilter', 'GenomeInfoDb', 'GenomicRanges', -#> 'gert', 'ggiraph', 'ggside', 'ggthemes', 'ggtree', 'ggtreeExtra', 'git2r', -#> 'gmp', 'graphlayouts', 'grImport2', 'gtools', 'haven', 'htmlTable', -#> 'htmlwidgets', 'httpuv', 'insight', 'interactiveDisplayBase', 'interp', -#> 'KEGGREST', 'later', 'lava', 'LEA', 'leaflet', 'leiden', 'limma', 'link2GI', -#> 'lintr', 'lme4', 'lpSolve', 'lpSolveAPI', 'Maaslin2', 'maps', 'markdown', -#> 'MAST', 'Matrix', 'MatrixModels', 'matrixStats', 'mclust', 'mia', -#> 'microbiome', 'microbiomeDataSets', 'MicrobiotaProcess', -#> 'MultiAssayExperiment', 'mvtnorm', 'network', 'nlme', 'NOISeq', 'ordinal', -#> 'osqp', 'pak', 'parameters', 'pcaPP', 'performance', 'plotrix', 'pls', -#> 'pracma', 'processx', 'progress', 'PROJ', 'qgraph', 'qs', 'R.utils', -#> 'rbibutils', 'RcppArmadillo', 'RcppEigen', 'Rdpack', 'report', 'Rfast', -#> 'rgl', 'rhdf5', 'rhdf5filters', 'rJava', 'Rmpfr', 'robustbase', 'rpart', -#> 'RSQLite', 'Rtsne', 's2', 'S4Vectors', 'sass', 'ScaledMatrix', 'scales', -#> 'scater', 'scuttle', 'segmented', 'SeqArray', 'seqinr', 'seriation', -#> 'Seurat', 'SeuratObject', 'shiny', 'shinybusy', 'SingleCellExperiment', -#> 'sna', 'sp', 'SparseArray', 'sparseMatrixStats', 'spatstat.data', -#> 'spatstat.explore', 'spatstat.linnet', 'spatstat.model', 'spatstat.random', -#> 'spatstat.sparse', 'spatstat.utils', 'spdep', 'stringdist', 'stringfish', -#> 'svglite', 'testthat', 'this.path', 'tinytex', 'TMB', 'treeio', -#> 'TreeSummarizedExperiment', 'units', 'V8', 'vroom', 'wesanderson', 'wk', -#> 'Wrench', 'XML', 'xml2', 'zCompositions', 'zinbwave', 'cluster' if (!require("devtools", quietly = TRUE)) { install.packages("devtools") } devtools::install_github("adrientaudiere/MiscMetabar", ref = "dev") -#> Downloading GitHub repo adrientaudiere/MiscMetabar@dev -#> -#> ── R CMD build ───────────────────────────────────────────────────────────────── -#> * checking for file ‘/tmp/RtmpOhxQ8G/remotes3c7b673226355/adrientaudiere-MiscMetabar-59ef25a/DESCRIPTION’ ... OK -#> * preparing ‘MiscMetabar’: -#> * checking DESCRIPTION meta-information ... OK -#> * checking for LF line-endings in source and make files and shell scripts -#> * checking for empty or unneeded directories -#> * building ‘MiscMetabar_0.51.tar.gz’ -#> Installation du package dans '/tmp/RtmpVdTtbP/temp_libpathd6864a1812db' -#> (car 'lib' n'est pas spécifié) ``` ## Some use of MiscMetabar @@ -284,11 +92,11 @@ more examples. For an introduction to metabarcoding in R, Please visite the [state of the field](https://adrientaudiere.github.io/MiscMetabar/articles/states_of_fields_in_R.html) -vignettes. The [import, export and track]() vignette explains how import -and export -. -Its also show how to summarize useful information (number of sequences, -samples and clusters) accross bioinformatic pipelines. +vignettes. The [import, export and +track](https://adrientaudiere.github.io/MiscMetabar/articles/import_export_track.html) +vignette explains how import and export `phyloseq` object. Its also show +how to summarize useful information (number of sequences, samples and +clusters) accross bioinformatic pipelines. If you are interested in ecological metrics, see the vignettes describing @@ -303,7 +111,7 @@ tutorial introduces the different way of clustering already-clustered OTU/ASV. The vignette [tengeler]() explore the dataset from Tengeler et al. (2020) using some MiscMetabar functions. -For developers, I also have a vignette describing som [rules of +For developers, I also wrote a vignette describing som [rules of codes](https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html). ### Summarize a physeq object @@ -322,8 +130,6 @@ summary_plot_pq(data_fungi) ``` r p <- MiscMetabar::hill_pq(data_fungi, variable = "Height") -#> Taxa are now in rows. -#> Cleaning suppress 0 taxa and 0 samples. p$plot_Hill_0 ``` From c2e7e906b09545aaf5b647aa4f4a2080b5c0732d Mon Sep 17 00:00:00 2001 From: Adrien Taudiere Date: Tue, 12 Dec 2023 12:19:05 +0100 Subject: [PATCH 7/7] style: improve page references from pkgdown site --- _pkgdown.yml | 155 ++++++++++++++++++++++++++++++++++++++++++++++ pkgdown/extra.css | 12 ++++ 2 files changed, 167 insertions(+) diff --git a/_pkgdown.yml b/_pkgdown.yml index a579225c..51dad1e3 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -38,6 +38,161 @@ navbar: - text: Rules of code href: articles/Rules.html +reference: +- title: Describe phyloseq object + contents: + - summary_plot_pq + - tbl_sum_samdata + - verify_pq + + +- title: Transform phyloseq object +- subtitle: Taxonomy + contents: + - add_funguild_info + - add_new_taxonomy_pq + - add_blast_info + - blast_to_phyloseq + - blast_pq + - blast_to_derep + - filter_asv_blast + +- subtitle: OTU table + contents: + - as_binary_otu_table + - asv2otu + - lulu_pq + - mumu_pq + - subset_taxa_pq + - subset_taxa_tax_control + +- subtitle: Sample datase + contents: + - subset_samples_pq + +- subtitle: Phylogenetic tree + contents: + - build_phytree_pq + +- subtitle: Others + contents: + - add_dna_to_phyloseq + - clean_pq + + +- title: Explore phyloseq object +- subtitle: alpha-diversity + contents: + - accu_plot + - accu_samp_threshold + - hill_pq + - hill_tuckey_pq + - iNEXT_pq + + +- subtitle: beta-diversity + contents: + - accu_samp_threshold + - adonis_pq + - biplot_pq + - circle_pq + - compare_pairs_pq + - ggvenn_pq + - graph_test_pq + - LCBD_pq + - multi_biplot_pq + - plot_LCBD_pq + - plot_tsne_pq + - ridges_pq + - sankey_pq + - SRS_curve_pq + - tsne_pq + - upset_pq + - upset_test_pq + - venn_pq + +- subtitle: Differencial abundance analysis + contents: + - multipatt_pq + - phyloseq_to_edgeR + - plot_edgeR_pq + - plot_deseq2_pq + - plot_mt + +- subtitle: Taxonomy + contents: + - heat_tree_pq + - krona + - merge_krona + - multitax_bar_pq + - plot_guild_pq + - plot_tax_pq + - rotl_pq + - search_exact_seq_pq + - tax_bar_pq + - tax_datatable + - treemap_pq + - vs_search_global + +- title: Improve reproducibility +- subtitle: Import/export phyloseq object + contents: + - read_pq + - save_pq + - write_pq +- subtitle: Track info along pipeline + contents: + - count_seq + - track_wkflow + - track_wkflow_samples +- subtitle: Utilities for [targets](https://books.ropensci.org/targets/) pipeline + contents: + - list_fastq_files + - rename_samples_otu_table + - select_one_sample + - simplify_taxo + - subsample_fastq + +- title: Datasets + contents: + - data_fungi + - data_fungi_sp_known + - Tengeler2020_pq + +- title: Others utilities + contents: + - all_object_size + - diff_fct_diff_class + - dist_bycol + - dist_pos_control + - funky_color + - get_file_extension + - install_pkg_needed + - multiplot + - perc + + + +- title: Deprecated + contents: + - adonis_phyloseq + - biplot_physeq + - clean_physeq + - ggVenn_phyloseq + - hill_phyloseq + - hill_tuckey_phyloseq + - lulu_phyloseq + - otu_circle + - physeq_graph_test + - physeq_heat_tree + - plot_deseq2_phyloseq + - plot_edgeR_phyloseq + - read_phyloseq + - sankey_phyloseq + - summary_plot_phyloseq + - venn_phyloseq + - write_phyloseq + development: mode: auto diff --git a/pkgdown/extra.css b/pkgdown/extra.css index c3e9c26c..9f1de4e7 100644 --- a/pkgdown/extra.css +++ b/pkgdown/extra.css @@ -31,3 +31,15 @@ .section { text-align: justify; } + +.template-reference-index h2 { + background-color: #c8a734; + border-radius: 20px; + padding: 12px; +} + +.template-reference-index h3 { + background-color: #c8a73440; + border-radius: 12px; + padding: 6px; +} \ No newline at end of file