Commit 82589719 authored by Midoux Cedric's avatar Midoux Cedric
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demo dataset

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EnvType Description FoodType
BHT0.LOT01 BoeufHache LOT1 Meat
BHT0.LOT03 BoeufHache LOT3 Meat
BHT0.LOT04 BoeufHache LOT4 Meat
BHT0.LOT05 BoeufHache LOT5 Meat
BHT0.LOT06 BoeufHache LOT6 Meat
BHT0.LOT07 BoeufHache LOT7 Meat
BHT0.LOT08 BoeufHache LOT8 Meat
BHT0.LOT10 BoeufHache LOT10 Meat
VHT0.LOT01 VeauHache LOT1 Meat
VHT0.LOT02 VeauHache LOT2 Meat
VHT0.LOT03 VeauHache LOT3 Meat
VHT0.LOT04 VeauHache LOT4 Meat
VHT0.LOT06 VeauHache LOT6 Meat
VHT0.LOT07 VeauHache LOT7 Meat
VHT0.LOT08 VeauHache LOT8 Meat
VHT0.LOT10 VeauHache LOT10 Meat
DLT0.LOT01 DesLardons LOT1 Meat
DLT0.LOT03 DesLardons LOT3 Meat
DLT0.LOT04 DesLardons LOT4 Meat
DLT0.LOT05 DesLardons LOT5 Meat
DLT0.LOT06 DesLardons LOT6 Meat
DLT0.LOT07 DesLardons LOT7 Meat
DLT0.LOT08 DesLardons LOT8 Meat
DLT0.LOT10 DesLardons LOT10 Meat
MVT0.LOT01 SaucisseVolaille LOT1 Meat
MVT0.LOT03 SaucisseVolaille LOT3 Meat
MVT0.LOT05 SaucisseVolaille LOT5 Meat
MVT0.LOT06 SaucisseVolaille LOT6 Meat
MVT0.LOT07 SaucisseVolaille LOT7 Meat
MVT0.LOT08 SaucisseVolaille LOT8 Meat
MVT0.LOT09 SaucisseVolaille LOT9 Meat
MVT0.LOT10 SaucisseVolaille LOT10 Meat
CDT0.LOT02 Crevette LOT2 Seafood
CDT0.LOT04 Crevette LOT4 Seafood
CDT0.LOT05 Crevette LOT5 Seafood
CDT0.LOT06 Crevette LOT6 Seafood
CDT0.LOT07 Crevette LOT7 Seafood
CDT0.LOT08 Crevette LOT8 Seafood
CDT0.LOT09 Crevette LOT9 Seafood
CDT0.LOT10 Crevette LOT10 Seafood
SFT0.LOT01 SaumonFume LOT1 Seafood
SFT0.LOT02 SaumonFume LOT2 Seafood
SFT0.LOT03 SaumonFume LOT3 Seafood
SFT0.LOT04 SaumonFume LOT4 Seafood
SFT0.LOT05 SaumonFume LOT5 Seafood
SFT0.LOT06 SaumonFume LOT6 Seafood
SFT0.LOT07 SaumonFume LOT7 Seafood
SFT0.LOT08 SaumonFume LOT8 Seafood
FST0.LOT01 FiletSaumon LOT1 Seafood
FST0.LOT02 FiletSaumon LOT2 Seafood
FST0.LOT03 FiletSaumon LOT3 Seafood
FST0.LOT05 FiletSaumon LOT5 Seafood
FST0.LOT06 FiletSaumon LOT6 Seafood
FST0.LOT07 FiletSaumon LOT7 Seafood
FST0.LOT08 FiletSaumon LOT8 Seafood
FST0.LOT10 FiletSaumon LOT10 Seafood
FCT0.LOT01 FiletCabillaud LOT1 Seafood
FCT0.LOT02 FiletCabillaud LOT2 Seafood
FCT0.LOT03 FiletCabillaud LOT3 Seafood
FCT0.LOT05 FiletCabillaud LOT5 Seafood
FCT0.LOT06 FiletCabillaud LOT6 Seafood
FCT0.LOT07 FiletCabillaud LOT7 Seafood
FCT0.LOT08 FiletCabillaud LOT8 Seafood
FCT0.LOT10 FiletCabillaud LOT10 Seafood
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demo/mach.tsv 0 → 100644
Run Project Time Bande sex mere Weaned
SF0901 3 Kinetic D14 1105 1 17MAG101814 TRUE
SF0931 3 Kinetic D14 1105 2 17MAG101827 TRUE
SF0951 3 Kinetic D14 1105 1 17MAG101855 TRUE
SF1011 3 Kinetic D14 1105 2 17MAG101965 TRUE
SF1031 3 Kinetic D14 1105 1 17MAG102029 TRUE
SF1831 3 Kinetic D14 1106 1 17MAG082150 TRUE
SF1861 3 Kinetic D14 1106 2 17MAG082210 TRUE
SF1871 3 Kinetic D14 1106 1 17MAG085889 TRUE
SF1911 3 Kinetic D14 1106 1 17MAG103303 TRUE
SF1931 3 Kinetic D14 1106 2 17MAG103313 TRUE
SF2641 3 Kinetic D14 1110 1 17MAG094915 TRUE
SF2671 3 Kinetic D14 1110 1 17MAG095009 TRUE
SF2721 3 Kinetic D14 1110 2 17MAG103324 TRUE
SF2741 3 Kinetic D14 1110 2 17MAG103300 TRUE
SF2751 3 Kinetic D14 1110 2 17MAG103609 TRUE
SF2801 3 Kinetic D14 1111 2 17MAG103836 TRUE
SF2821 3 Kinetic D14 1111 2 17MAG103881 TRUE
SF2881 3 Kinetic D14 1111 1 17MAG103898 TRUE
SF2921 3 Kinetic D14 1111 2 17MAG104167 TRUE
SF2941 3 Kinetic D14 1111 1 17MAG104190 TRUE
SF4481 3 Kinetic D14 1112 1 17MAG104203 TRUE
SF4491 3 Kinetic D14 1112 1 17MAG104634 TRUE
SF4521 3 Kinetic D14 1112 2 17MAG105122 TRUE
SF4541 3 Kinetic D14 1112 2 17MAG104818 TRUE
SF4581 3 Kinetic D14 1112 1 17MAG105040 TRUE
SF5181 3 Kinetic D14 1113 1 17MAG105121 TRUE
SF5201 3 Kinetic D14 1113 1 17MAG104194 TRUE
SF5231 3 Kinetic D14 1113 1 17MAG095083 TRUE
SF5261 3 Kinetic D14 1113 2 17MAG103303 TRUE
SF5271 3 Kinetic D14 1113 2 17MAG103313 TRUE
SF5301 3 Kinetic D14 1113 2 17MAG105042 TRUE
SF0902 3 Kinetic D36 1105 1 17MAG101814 FALSE
SF0932 3 Kinetic D36 1105 2 17MAG101827 FALSE
SF0952 3 Kinetic D36 1105 1 17MAG101855 FALSE
SF1012 3 Kinetic D36 1105 2 17MAG101965 FALSE
SF1032 3 Kinetic D36 1105 1 17MAG102029 FALSE
SF1832 3 Kinetic D36 1106 1 17MAG082150 FALSE
SF1862 3 Kinetic D36 1106 2 17MAG082210 FALSE
SF1872 3 Kinetic D36 1106 1 17MAG085889 FALSE
SF1912 3 Kinetic D36 1106 1 17MAG103303 FALSE
SF1932 3 Kinetic D36 1106 2 17MAG103313 FALSE
SF2642 3 Kinetic D36 1110 1 17MAG094915 FALSE
SF2672 3 Kinetic D36 1110 1 17MAG095009 FALSE
SF2722 3 Kinetic D36 1110 2 17MAG103324 FALSE
SF2742 3 Kinetic D36 1110 2 17MAG103300 FALSE
SF2752 3 Kinetic D36 1110 2 17MAG103609 FALSE
SF2802 3 Kinetic D36 1111 2 17MAG103836 FALSE
SF2822 3 Kinetic D36 1111 2 17MAG103881 FALSE
SF2882 3 Kinetic D36 1111 1 17MAG103898 FALSE
SF2922 3 Kinetic D36 1111 2 17MAG104167 FALSE
SF2942 3 Kinetic D36 1111 1 17MAG104190 FALSE
SF4482 3 Kinetic D36 1112 1 17MAG104203 FALSE
SF4492 3 Kinetic D36 1112 1 17MAG104634 FALSE
SF4522 3 Kinetic D36 1112 2 17MAG105122 FALSE
SF4542 3 Kinetic D36 1112 2 17MAG104818 FALSE
SF4582 3 Kinetic D36 1112 1 17MAG105040 FALSE
SF5182 3 Kinetic D36 1113 1 17MAG105121 FALSE
SF5202 3 Kinetic D36 1113 1 17MAG104194 FALSE
SF5232 3 Kinetic D36 1113 1 17MAG095083 FALSE
SF5262 3 Kinetic D36 1113 2 17MAG103303 FALSE
SF5272 3 Kinetic D36 1113 2 17MAG103313 FALSE
SF5302 3 Kinetic D36 1113 2 17MAG105042 FALSE
SF0903 3 Kinetic D48 1105 1 17MAG101814 FALSE
SF0933 3 Kinetic D48 1105 2 17MAG101827 FALSE
SF0953 3 Kinetic D48 1105 1 17MAG101855 FALSE
SF1013 3 Kinetic D48 1105 2 17MAG101965 FALSE
SF1033 3 Kinetic D48 1105 1 17MAG102029 FALSE
SF1833 3 Kinetic D48 1106 1 17MAG082150 FALSE
SF1863 3 Kinetic D48 1106 2 17MAG082210 FALSE
SF1873 3 Kinetic D48 1106 1 17MAG085889 FALSE
SF1913 3 Kinetic D48 1106 1 17MAG103303 FALSE
SF1933 3 Kinetic D48 1106 2 17MAG103313 FALSE
SF2643 3 Kinetic D48 1110 1 17MAG094915 FALSE
SF2673 3 Kinetic D48 1110 1 17MAG095009 FALSE
SF2723 3 Kinetic D48 1110 2 17MAG103324 FALSE
SF2743 3 Kinetic D48 1110 2 17MAG103300 FALSE
SF2753 3 Kinetic D48 1110 2 17MAG103609 FALSE
SF2803 3 Kinetic D48 1111 2 17MAG103836 FALSE
SF2823 3 Kinetic D48 1111 2 17MAG103881 FALSE
SF2883 3 Kinetic D48 1111 1 17MAG103898 FALSE
SF2923 3 Kinetic D48 1111 2 17MAG104167 FALSE
SF2943 3 Kinetic D48 1111 1 17MAG104190 FALSE
SF4483 3 Kinetic D48 1112 1 17MAG104203 FALSE
SF4493 3 Kinetic D48 1112 1 17MAG104634 FALSE
SF4523 3 Kinetic D48 1112 2 17MAG105122 FALSE
SF4543 3 Kinetic D48 1112 2 17MAG104818 FALSE
SF4583 3 Kinetic D48 1112 1 17MAG105040 FALSE
SF5183 3 Kinetic D48 1113 1 17MAG105121 FALSE
SF5203 3 Kinetic D48 1113 1 17MAG104194 FALSE
SF5233 3 Kinetic D48 1113 1 17MAG095083 FALSE
SF5263 3 Kinetic D48 1113 2 17MAG103303 FALSE
SF5273 3 Kinetic D48 1113 2 17MAG103313 FALSE
SF5303 3 Kinetic D48 1113 2 17MAG105042 FALSE
SF0904 3 Kinetic D60 1105 1 17MAG101814 FALSE
SF0934 3 Kinetic D60 1105 2 17MAG101827 FALSE
SF0954 3 Kinetic D60 1105 1 17MAG101855 FALSE
SF1014 3 Kinetic D60 1105 2 17MAG101965 FALSE
SF1034 3 Kinetic D60 1105 1 17MAG102029 FALSE
SF1834 3 Kinetic D60 1106 1 17MAG082150 FALSE
SF1864 3 Kinetic D60 1106 2 17MAG082210 FALSE
SF1874 3 Kinetic D60 1106 1 17MAG085889 FALSE
SF1914 3 Kinetic D60 1106 1 17MAG103303 FALSE
SF1934 3 Kinetic D60 1106 2 17MAG103313 FALSE
SF2644 3 Kinetic D60 1110 1 17MAG094915 FALSE
SF2674 3 Kinetic D60 1110 1 17MAG095009 FALSE
SF2724 3 Kinetic D60 1110 2 17MAG103324 FALSE
SF2744 3 Kinetic D60 1110 2 17MAG103300 FALSE
SF2754 3 Kinetic D60 1110 2 17MAG103609 FALSE
SF2804 3 Kinetic D60 1111 2 17MAG103836 FALSE
SF2824 3 Kinetic D60 1111 2 17MAG103881 FALSE
SF2884 3 Kinetic D60 1111 1 17MAG103898 FALSE
SF2924 3 Kinetic D60 1111 2 17MAG104167 FALSE
SF2944 3 Kinetic D60 1111 1 17MAG104190 FALSE
SF4484 3 Kinetic D60 1112 1 17MAG104203 FALSE
SF4494 3 Kinetic D60 1112 1 17MAG104634 FALSE
SF4524 3 Kinetic D60 1112 2 17MAG105122 FALSE
SF4544 3 Kinetic D60 1112 2 17MAG104818 FALSE
SF4584 3 Kinetic D60 1112 1 17MAG105040 FALSE
SF5184 3 Kinetic D60 1113 1 17MAG105121 FALSE
SF5204 3 Kinetic D60 1113 1 17MAG104194 FALSE
SF5234 3 Kinetic D60 1113 1 17MAG095083 FALSE
SF5264 3 Kinetic D60 1113 2 17MAG103303 FALSE
SF5274 3 Kinetic D60 1113 2 17MAG103313 FALSE
SF5304 3 Kinetic D60 1113 2 17MAG105042 FALSE
SF0905 3 Kinetic D70 1105 1 17MAG101814 FALSE
SF0935 3 Kinetic D70 1105 2 17MAG101827 FALSE
SF0955 3 Kinetic D70 1105 1 17MAG101855 FALSE
SF1015 3 Kinetic D70 1105 2 17MAG101965 FALSE
SF1035 3 Kinetic D70 1105 1 17MAG102029 FALSE
SF1835 3 Kinetic D70 1106 1 17MAG082150 FALSE
SF1865 3 Kinetic D70 1106 2 17MAG082210 FALSE
SF1875 3 Kinetic D70 1106 1 17MAG085889 FALSE
SF1915 3 Kinetic D70 1106 1 17MAG103303 FALSE
SF1935 3 Kinetic D70 1106 2 17MAG103313 FALSE
SF2645 3 Kinetic D70 1110 1 17MAG094915 FALSE
SF2675 3 Kinetic D70 1110 1 17MAG095009 FALSE
SF2725 3 Kinetic D70 1110 2 17MAG103324 FALSE
SF2745 3 Kinetic D70 1110 2 17MAG103300 FALSE
SF2755 3 Kinetic D70 1110 2 17MAG103609 FALSE
SF2805 3 Kinetic D70 1111 2 17MAG103836 FALSE
SF2825 3 Kinetic D70 1111 2 17MAG103881 FALSE
SF2885 3 Kinetic D70 1111 1 17MAG103898 FALSE
SF2925 3 Kinetic D70 1111 2 17MAG104167 FALSE
SF2945 3 Kinetic D70 1111 1 17MAG104190 FALSE
SF4485 3 Kinetic D70 1112 1 17MAG104203 FALSE
SF4495 3 Kinetic D70 1112 1 17MAG104634 FALSE
SF4525 3 Kinetic D70 1112 2 17MAG105122 FALSE
SF4545 3 Kinetic D70 1112 2 17MAG104818 FALSE
SF4585 3 Kinetic D70 1112 1 17MAG105040 FALSE
SF5185 3 Kinetic D70 1113 1 17MAG105121 FALSE
SF5205 3 Kinetic D70 1113 1 17MAG104194 FALSE
SF5235 3 Kinetic D70 1113 1 17MAG095083 FALSE
SF5265 3 Kinetic D70 1113 2 17MAG103303 FALSE
SF5275 3 Kinetic D70 1113 2 17MAG103313 FALSE
SF5305 3 Kinetic D70 1113 2 17MAG105042 FALSE
library(phyloseq)
data("GlobalPatterns")
food <-
import_biom(
BIOMfilename = "chaillou.biom",
treefilename = "chaillou.nwk",
parseFunction = parse_taxonomy_greengenes
)
sample_data(food) <-
read.table("chaillou.tsv",
header = TRUE,
row.names = 1,
sep = "\t")
kinetic <-
import_biom(BIOMfilename = "mach.biom", treefilename = "mach.nwk")
sample_data(kinetic) <-
read.table("mach.tsv",
header = TRUE,
row.names = 1,
sep = "\t")
colnames(tax_table(kinetic)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus")
tax_table(kinetic)[grep("unknown ", tax_table(kinetic))] <- NA
ravel <-
import_biom(BIOMfilename = "ravel.biom")
sample_data(ravel) <-
read.table("ravel.tsv",
header = TRUE,
row.names = 1,
sep = "\t")
colnames(tax_table(ravel)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")
tax_table(ravel)[grep("unknown ", tax_table(ravel))] <- NA
soil <-
import_biom(BIOMfilename = "morton.biom", treefilename = "morton.tree")
sample_data(soil) <-
read.table("morton.csv",
header = TRUE,
row.names = 1,
sep = "\t")
colnames(tax_table(soil)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")
tax_table(soil)[grep("unknown ", tax_table(soil))] <- NA
biorare <-
import_biom(BIOMfilename = "biorare.biom", treefilename = "biorare.nwk")
sample_data(biorare) <-
read.table("biorare.tsv", header = TRUE, row.names = 1)
colnames(tax_table(biorare)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")
tax_table(biorare)[grep("unknown ", tax_table(biorare))] <- NA
# cellulose <- import_biom(BIOMfilename = "cellulose.biom")
# sample_data(cellulose) <- read.table("cellulose.tsv", header = TRUE, row.names = 1)
save(GlobalPatterns, food, kinetic, soil, ravel, biorare, file = "demo.RData")
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demo/ravel.tsv 0 → 100644
Ethnic_Group pH Nugent_Score Nugent_Cat CST Depth RealDepth
S001 Asian 4 0 low I 2329 2335
S002 White 4 0 low II 1400 1403
S003 Black 4 1 low III 1378 1376
S004 Asian 4.7 0 low I 2273 2286
S005 Black 5 6 intermediate IV 1713 1705
S006 White 4 0 low I 1822 1817
S007 White 4.7 1 low II 1961 1942
S008 White 5.8 9 high IV 1872 1863
S009 White 4.4 0 low III 2142 2142
S010 Black 4.4 1 low I 1823 1821
S011 White 4 0 low III 2080 2080
S012 White 5 10 high IV 1598 1586
S013 White 4.7 0 low III 5277 5283
S014 Black 4.4 2 low II 5262 5262
S015 White 4.4 0 low I 1998 1994
S016 White 5.8 1 low III 2008 2002
S017 Asian 7 5 intermediate III 2352 2362
S018 Black 4 0 low I 3765 3761
S019 Black 4 0 low III 2001 1994
S020 Hispanic 4 0 low III 1799 1797
S021 Black 4.7 1 low II 1448 1449
S022 White 5 1 low V 2147 2139
S023 Black 7 8 high IV 3285 3284
S024 Black 4 0 low III 1785 1780
S025 Black 5 10 high IV 2586 2595
S026 Black 4.4 0 low I 2658 2658
S027 Black 4 0 low I 2294 2296
S028 Black 5.5 4 intermediate IV 1407 1405
S029 White 4 0 low I 2470 2471
S030 Black 5.8 9 high IV 2116 2116
S031 Black 5 8 high IV 1847 1837
S032 White 4 0 low I 2142 2143
S033 White 4.4 0 low III 2431 2434
S034 Hispanic 4 0 low I 2337 2340
S035 Hispanic 5 1 low IV 1978 1972
S036 Hispanic 4.4 2 low I 2456 2474
S037 Hispanic 4 0 low I 1273 1271
S038 Hispanic 5.5 7 high IV 1797 1791
S039 Hispanic 5.3 8 high IV 1738 1731
S040 Hispanic 4.7 0 low III 1660 1660
S041 Hispanic 4.4 1 low III 1365 1362
S042 Hispanic 5.5 9 high IV 2475 2489
S043 Hispanic 4 1 low V 2010 2006
S044 Hispanic 4.4 0 low IV 3069 3064
S045 Hispanic 5.5 7 high IV 1902 1887
S046 Hispanic 4 1 low III 2263 2262
S047 White 5.3 10 high III 1667 1665
S048 Hispanic 5 9 high IV 2033 2017
S049 Hispanic 4.7 7 high IV 1302 1300
S050 Hispanic 4 1 low III 1425 1425
S051 Hispanic 5.5 8 high IV 2146 2148
S052 Hispanic 5.3 4 intermediate II 2228 2237
S053 Hispanic 5 8 high IV 1682 1666
S054 Hispanic 4.4 0 low III 2202 2201
S055 Hispanic 4 0 low I 1697 1695
S056 Hispanic 5 0 low I 1845 1841
S057 Hispanic 5.5 3 low IV 1553 1548
S058 Hispanic 4 0 low I 1465 1468
S059 Hispanic 4 0 low III 2259 2265
S060 Hispanic 4 0 low III 1767 1762
S061 Hispanic 4 4 intermediate II 774 774
S062 Hispanic 5.8 8 high IV 1676 1667
S063 Hispanic 5.4 7 high II 1045 1045
S064 Hispanic 5.4 8 high IV 2292 2298
S065 Hispanic 4 0 low I 2262 2262
S066 White 4 0 low III 1844 1838
S067 Asian 4 0 low I 1585 1583
S068 White 4 6 intermediate III 2523 2518
S069 White 4 3 low I 1209 1207
S070 Black 5 10 high IV 1834 1825
S071 Black 5 0 low III 1575 1566
S072 Black 5.5 10 high III 1848 1835
S073 Asian 5.3 9 high IV 1524 1515
S074 White 4.4 0 low I 1742 1740
S075 Asian 4 1 low III 1905 1900
S076 White 4.7 4 intermediate II 1336 1328
S077 Asian 4 3 low III 1825 1822
S078 White 4 0 low I 1607 1604
S079 Black 4 0 low I 2221 2224
S080 White 4 0 low I 2385 2390
S081 Asian 4 0 low V 936 936
S082 White 4 0 low I 1519 1511
S083 White 5 2 low V 1512 1508
S084 Black 4 0 low I 1681 1676
S085 Black 5.5 10 high IV 1987 1952
S086 White 4.7 3 low V 1262 1261
S087 White 4.4 0 low I 1795 1788
S088 White 5.3 2 low III 2662 2668
S089 White 5.5 0 low I 2789 2791
S090 White 4 2 low IV 2390 2401
S091 Black 4 1 low III 2555 2556
S092 White 4 1 low I 1255 1254
S093 White 5 4 intermediate I 1715 1705
S094 Black 4 0 low I 2309 2310
S095 Black 4 0 low I 2693 2696
S096 White 5 4 intermediate II 1911 1906
S097 Black 4.4 1 low I 2979 2982
S098 White 5 0 low V 1017 1016
S099 White 4.7 2 low I 2302 2309
S100 Black 4 0 low I 3741 3742
S101 White 4.4 0 low III 2556 2558
S102 Black 5 9 high IV 2001 1986
S103 Black 4 0 low I 1955 1950
S104 Black 5 5 intermediate IV 2799 2807
S105 Black 5.5 9 high IV 2702 2704
S106 Black 4.4 0 low I 2931 2930
S107 White 4 0 low I 2681 2681
S108 Black 4 0 low I 2402 2404
S109 Black 5.8 8 high IV 2762 2764
S110 Black 5.5 10 high III 2103 2098
S111 Black 4 0 low I 3146 3144
S112 White 4 1 low I 693 693
S113 White 4.4 0 low V 2514 2517
S114 White 5.8 8 high IV 2689 2697
S115 Black 4 2 low I 2617 2625
S116 Black 4 0 low I 3342 3339
S117 White 4 1 low I 3490 3495
S118 Black 5 1 low II 1984 1971
S119 Black 4 1 low III 2073 2070
S120 White 4 0 low I 2428 2438
S121 Hispanic 4.7 0 low V 1046 1046
S122 Black 4 0 low I 2078 2074
S123 Black 4.7 9 high III 2576 2583
S124 White 4 0 low I 3216 3218
S125 White 4 0 low I 3060 3064
S126 Hispanic 4 0 low I 3439 3440
S127 White 4.4 2 low V 2820 2830
S128 Asian 4.4 0 low I 2340 2348
S129 Asian 4 8 high IV 2103 2101
S130 Black 5 10 high IV 3070 3073
S131 White 5 0 low III 2568 2571
S132 White 4 0 low III 2867 2870
S133 Hispanic 5 0 low III 2975 2983
S134 Hispanic 5.5 8 high IV 2620 2624
S135 Hispanic 5 1 low III 1935 1917
S136 Hispanic 5 1 low III 3792 3788
S137 Hispanic 4.5 4 intermediate IV 881 881
S138 Hispanic 5.8 10 high IV 3075 3073
S139 Hispanic 4.4 0 low I 2219 2230
S140 Hispanic 5.5 9 high IV 2460 2478
S141 Hispanic 5.3 8 high IV 2101 2099
S142 Hispanic 5 1 low III 3726 3725
S143 Hispanic 5.5 8 high IV 3829 3815
S144 Hispanic 5.5 8 high IV 1624 1619
S145 Hispanic 5 3 low IV 2075 2068
S146 Hispanic 5 4 intermediate II 2352 2356
S147 Hispanic 7 7 high IV 2330 2345
S148 Hispanic 4.4 0 low III 1877 1875
S149 Hispanic 5.5 5 intermediate III 2285 2283
S150 Hispanic 5 4 intermediate III 2964 2965
S151 Hispanic 4.7 8 high IV 5057 5063
S152 Hispanic 5 4 intermediate IV 2353 2366
S153 Hispanic 4.4 0 low III 2548 2552
S154 Hispanic 4.4 5 intermediate III 2095 2091
S155 Hispanic 4.7 8 high III 2958 2969
S156 Hispanic 4.7 1 low III 3408 3412
S157 Hispanic 5.3 1 low III 2099 2096
S158 Hispanic 5.3 7 high III 2456 2468
S159 Hispanic 5 8 high IV 2795 2796
S160 Hispanic 5 0 low IV 2308 2326
S161 Hispanic 5.5 4 intermediate III 2915 2917
S162 Hispanic 5 2 low III 3003 3003
S163 Hispanic 5 0 low V 3517 3515
S164 Hispanic 4.7 0 low III 2699 2705
S165 Hispanic 4.4 1 low III 2766 2764
S166 Hispanic 4.4 0 low III 2972 2975
S167 Hispanic 4.4 1 low III 3855 3854
S168 Hispanic 4.4 0 low I 2573 2571
S169 Hispanic 5 5 intermediate II 1449 1453
S170 Hispanic 4.7 1 low III 2801 2806
S171 Hispanic 4.4 0 low III 2126 2121
S172 Hispanic 5.3 10 high IV 2515 2511
S173 Hispanic 4.7 1 low V 2069 2065
S174 Hispanic 5.8 8 high IV 2464 2463
S175 Hispanic 5.3 7 high IV 5710 5713
S176 Hispanic 4.4 6 intermediate IV 3276 3290
S177 Hispanic 5 7 high IV 2016 2004
S178 Hispanic 5.5 5 intermediate IV 4338 4336
S179 Hispanic 7 8 high IV 3002 2997
S180 Hispanic 4.4 1 low III 2619 2622
S181 Hispanic 4 0 low I 2289 2297
S182 Hispanic 4 0 low I 2290 2297
S183 Hispanic 4.4 5 intermediate III 1925 1908
S184 Hispanic 4 4 intermediate II 2804 2810
S185 Hispanic 5 8 high IV 2597 2593
S186 Hispanic 5.3 8 high IV 2634 2636
S187 Hispanic 4 8 high III 3672 3668
S188 Hispanic 5.5 10 high IV 7361 7392
S189 Asian 4 1 low III 2571 2573
S190 Hispanic 4 0 low I 2101 2100
S191 White 4.4 0 low I 1837 1830
S192 Black 5.5 8 high IV 1822 1813
S193 Hispanic 4 1 low I 2013 2007
S194 Asian 4.7 0 low I 1858 1849
S195 Black 5 5 intermediate V 1803 1792
S196 White 4 0 low I 2026 2021
S197 White 4 1 low I 1868 1866
S198 White 4 0 low I 2229 2233
S199 Black 5 10 high IV 2178 2171
S200 Black 4 1 low III 3387 3391
S201 Asian 4.7 0 low I 3165 3172
S202 Black 5.5 7 high IV 2306 2314
S203 White 4 1 low III 2777 2779
S204 Black 4 1 low III 2410 2411
S205 White 4 4 intermediate III 2638 2643
S206 White 7 6 intermediate II 2062 2051
S207 Black 4 1 low I 2199 2195
S208 White 5 7 high III 2297 2295
S209 Black 5.3 10 high IV 2119 2115
S210 White 4 0 low I 2218 2215
S211 White 5 3 low II 2284 2287
S212 Black 4 1 low I 3633 3631
S213 Asian 5 1 low III 3126 3128
S214 Black 4 0 low III 2475 2480
S215 White 5 7 high III 2403 2408
S216 White 4.4 1 low I 2874 2882
S217 Black 5 8 high III 2354 2362
S218 White 4 1 low III 4343 4339
S219 White 4 1 low III 2426 2432
S220 White 4 6 intermediate III 2448 2457
S221 Black 5.5 0 low III 2132 2130
S222 White 4 0 low I 2481 2482
S223 Asian 4 0 low III 2031 2026
S224 White 7 7 high IV 2979 2990
S225 White 4 3 low I 1986 1967
S226 White 4 0 low I 2028 2024
S227 Black 4 3 low III 2159 2156
S228 Black 5 5 intermediate III 1891 1884
S229 Black 5.5 10 high IV 1703 1685
S230 Black 4 1 low II 1830 1820
S231 Black 4 3 low I 1746 1735
S232 Asian 4 0 low I 1673 1663
S233 White 4 0 low I 2002 1994
S234 Black 4.7 0 low III 2139 2131
S235 Black 4.4 0 low III 2372 2373
S236 Asian 4.4 0 low I 2334 2339
S237 Black 4 0 low III 2210 2208
S238 Black 4 0 low III 1892 1883
S239 Black 5.5 10 high IV 1563 1553
S240 White 4 0 low I 2177 2169
S241 Black 4 0 low III 2059 2058
S242 Black 4.7 1 low III 1862 1848
S243 Black 5.8 9 high IV 1736 1736
S244 Black 5.3 10 high IV 1829 1812
S245 White 4.4 0 low I 1836 1831
S246 White 4.4 1 low V 2267 2278
S247 White 5 0 low I 2814 2814
S248 Black 4.7 4 intermediate III 1771 1760
S249 White 4 0 low III 2188 2185
S250 Asian 5.5 7 high IV 1830 1823
S251 Black 4.7 0 low II 1792 1784
S252 Black 4.7 0 low III 1489 1494
S253 Black 5 10 high IV 1478 1484
S254 Black 4 1 low III 1589 1578
S255 Black 5.3 8 high IV 1870 1862
S256 White 4 0 low I 1774 1761
S257 Black 5 0 low III 1678 1675
S258 White 4 0 low V 1806 1795
S259 Black 5.8 8 high IV 1604 1598
S260 Asian 4 0 low III 1700 1695
S261 Black 5.3 8 high IV 1817 1794
S262 White 4 0 low I 2695 2695
S263 Black 5.8 8 high IV 2457 2456
S264 White 4 0 low I 2163 2163
S265 Hispanic 4 1 low III 1716 1711
S266 Hispanic 4.4 0 low III 2092 2088
S267 White 4.7 3 low III 1851 1838
S268 Black 4.4 0 low I 1882 1877
S269 White 5.8 8 high IV 2549 2544
S270 Black 5 8 high IV 2600 2607
S271 White 5.5 8 high IV 3045 3044
S272 Asian 4.4 1 low I 2239 2242
S273 Asian 5 8 high IV 2704 2703
S274 White 4.4 0 low III 2143 2144
S275 Asian 4 1 low III 2164 2160
S276 White 5 1 low II 3888 3892
S277 White 4 0 low I 2093 2090
S278 White 4.4 5 intermediate III 1968 1961
S279 Black 5.5 9 high IV 2748 2758
S280 White 4.7 4 intermediate IV 2627 2631
S281 Black 4 3 low I 2517 2516
S282 Asian 4 3 low III 2320 2322
S283 Asian 4 2 low III 2067 2065
S284 White 4 0 low IV 1724 1714
S285 White 4.7 4 intermediate II 1657 1659
S286 Asian 5.5 4 intermediate II 1006 1006
S287 Asian 4 1 low I 2043 2033
S288 Asian 4.4 4 intermediate V 1772 1769
S289 Asian 5 1 low III 2303 2302
S290 Black 5 9 high IV 2194 2180
S291 White 4 0 low I 2170 2170
S292 Black 5.5 8 high IV 2067 2064
S293 White 4 0 low III 2086 2083
S294 White 4.4 2 low I 2067 2060
S295 Asian 4.7 0 low III 2396 2400
S296 Asian 4 4 intermediate V 1915 1915
S297 White 4 0 low I 2025 2024
S298 Asian 4 2 low III 2297 2300
S299 White 5 0 low V 2224 2233
S300 Asian 4 0 low III 2209 2209
S301 Asian 5.5 7 high IV 2393 2402
S302 Asian 4 1 low III 2203 2203
S303 Asian 5.3 1 low III 2404 2405
S304 Asian 4 0 low I 2353 2354
S305 Asian 5.8 3 low IV 1568 1560
S306 Hispanic 4 2 low III 2281 2280
S307 Black 5.3 6 intermediate III 2330 2334
S308 Black 5.5 10 high IV 2239 2257
S309 Hispanic 5.5 6 intermediate II 2127 2122
S310 Black 4.7 10 high IV 3109 3115
S311 Black 5.3 4 intermediate IV 1777 1770
S312 Black 4 0 low I 2108 2105
S313 Black 5.5 8 high IV 2962 2964
S314 Black 5 9 high IV 2470 2483
S315 Black 4.7 6 intermediate IV 2116 2106
S316 Black 4.7 7 high IV 2358 2368
S317 Black 4 0 low III 1938 1923
S318 Black 4 4 intermediate III 2345 2344
S319 Black 4 1 low III 2961 2964
S320 Black 4 0 low III 2766 2763
S321 Black 4.4 9 high IV 2641 2647
S322 Black 5 7 high IV 2247 2252
S323 Black 4 0 low III 2123 2122
S324 Asian 4.7 0 low III 1976 1974
S325 White 4 0 low I 1853 1840
S326 White 5.5 3 low I 2479 2485
S327 Black 5.5 10 high IV 1691 1691
S328 Black 5 8 high III 2223 2221
S329 Black 5 8 high IV 2221 2249
S330 Black 5.8 10 high IV 2019 1998
S331 Hispanic 5 8 high IV 2454 2475
S332 Asian 5 5 intermediate II 2742 2750
S333 Asian 4.4 0 low I 2308 2313
S334 Asian 4 2 low III 2056 2053
S335 Asian 4 0 low I 2046 2043
S336 Asian 4 0 low I 1664 1661
S337 Asian 5.8 5 intermediate IV 1972 1952
S338 Asian 4 2 low III 2157 2156
S339 Asian 4.4 0 low III 2029 2026
S340 Asian 4 0 low I 2284 2287
S341 Asian 4.4 0 low V 2227 2232
S342 Asian 4 0 low III 2525 2527
S343 Asian 5.5 1 low III 1939 1928
S344 Asian 4.7 7 high IV 2198 2189
S345 Asian 5.8 1 low II 1888 1867
S346 Asian 4.4 0 low I 1833 1830
S347 White 5.5 8 high IV 1796 1784
S348 Asian 5 6 intermediate V 1571 1561
S349 Asian 5.5 0 low III 1721 1717
S350 Asian 5 4 intermediate IV 1468 1474
S351 Asian 4.4 6 intermediate III 1274 1271
S352 Asian 5 4 intermediate I 1814 1799
S353 Asian 4.7 1 low III 1826 1817
S354 Asian 4.7 0 low V 1963 1959
S355 Asian 4 1 low III 1890 1886
S356 White 4 0 low I 1674 1665
S357 White 4 0 low III 1709 1704
S358 White 4 0 low I 1863 1858
S359 White 4 0 low III 1409 1409
S360 Asian 5.8 4 intermediate IV 1655 1648
S361 Asian 4 0 low I 1986 1980
S362 Asian 5 8 high III 2145 2149
S363 Asian 4 0 low III 2329 2335
S364 Asian 4 1 low III 3437 3429
S365 Asian 5 1 low III 2459 2462
S366 Asian 4 7 high III 2564 2565
S367 Asian 4.4 0 low I 2476 2478
S368 Asian 5.8 8 high IV 1949 1934
S369 Asian 5.8 4 intermediate IV 2049 2046
S370 Asian 4.4 7 high IV 1244 1245
S371 Asian 4 2 low III 1922 1917
S372 Asian 4.7 0 low III 2026 2021
S373 Asian 4.4 0 low III 2230 2237
S374 Asian 4 0 low III 2257 2259
S375 Asian 4.4 5 intermediate II 3336 3341
S376 Asian 4.4 0 low I 2790 2792
S377 Asian 4.4 0 low I 2611 2619
S378 Asian 4.4 3 low V 2229 2237
S379 Asian 4.4 0 low II 2155 2146
S380 Asian 4.7 8 high IV 2181 2174
S381 Asian 5.5 8 high IV 2232 2240
S382 Asian 4.7 1 low I 1919 1913
S383 Asian 5.8 7 high IV 2200 2199
S384 Asian 5.8 1 low IV 925 925
S385 Asian 4 2 low III 2356 2356
S386 Asian 4 1 low I 2372 2375
S387 Asian 4 3 low I 1983 1960
S388 Asian 5 3 low IV 1875 1852
S389 Asian 4.4 0 low III 1820 1810
S390 Asian 7 6 intermediate III 1873 1866
S391 Asian 4.4 0 low III 1733 1731
S392 Asian 4.4 0 low IV 1969 1967
S393 Asian 4.4 0 low III 1685 1682
S394 Asian 4.4 2 low III 1728 1725
This diff is collapsed.
......@@ -2,6 +2,23 @@ library(shinydashboard)
shinyUI(dashboardPage(
dashboardHeader(title = "Easy16S"),
dashboardSidebar(
tags$div(
title = "Load data for demo",
selectInput(
"demo",
label = "Select demo data",
choices = list(
"Input data" = "input",
"Chaillou et al., 2015" = "food",
"Mach et al., 2015" = "kinetic",
"Morton et al., 2017" = "soil",
"Ravel et al., 2011" = "ravel"#,
#"biorare"
),
selected = 1
)
),
hr(width = "90%"),
tags$div(
title = "Fichier d'abondance au format BIOM produit avec FROGS avec 'FROGS BIOM to std BIOM'",
fileInput(
......@@ -95,7 +112,6 @@ shinyUI(dashboardPage(
width = NULL, tabsetPanel(
tabPanel(
"Courbes",
htmlOutput("rarefaction"),
plotOutput("richnessA", height = 700),
uiOutput("richnessAUI")
),
......@@ -146,7 +162,11 @@ shinyUI(dashboardPage(
plotOutput("Heatmap", height = 700),
uiOutput("HeatmapUI")
),
tabPanel("Analyses multivariées", plotOutput("acp", height = 700), uiOutput("acpUI")),
tabPanel(
"Analyses multivariées",
plotOutput("acp", height = 700),
uiOutput("acpUI")
),
tabPanel(
"et plus ...",
div(
......@@ -156,4 +176,4 @@ shinyUI(dashboardPage(
)
)
)
))
\ No newline at end of file
))
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