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darmitage/cyanodiversity

Created November 1, 2011 20:56
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Phylodiversity plots
Raw
cyanodiversity
#This is code for those plots I made using the MPD and MNTD metrics. You need to organize them into a table such as the one below#
require(ggplot2)
data = read.csv("data.csv", header = TRUE, sep = "")
s <- c("NM1","NM2","NM3", "NM4", "NM5", "Green", "Pink", "Brown", "S1", "S2", "G1", "G2")
data$OTU <- factor(data$OTU)
cyanos = subset(data, group == "cyano")
PSBs = subset(data, group == "PSB")
closts = subset(data, group == "clost")
###############################################################################################
cyplot <- ggplot(cyanos, aes(layer,z, group=c(age,type)))+
geom_vline(xintercept = c(1), colour = "darkolivegreen2", size = 10)+
geom_vline(xintercept = c(2), colour = "palevioletred1", size = 10)+
geom_vline(xintercept = c(3), colour = "burlywood3", size = 10)+
geom_vline(xintercept = c(4), colour = "ivory3", size = 10)+
geom_vline(xintercept = c(5), colour = "ivory4", size = 10)+
geom_vline(xintercept = c(6), colour = "darkolivegreen4", size = 10)+
geom_vline(xintercept = c(7), colour = "palevioletred3", size = 10)+
geom_vline(xintercept = c(8), colour = "burlywood4", size = 10)+
geom_vline(xintercept = c(9), colour = "ivory3", size = 10)+
geom_vline(xintercept = c(10), colour = "ivory4", size = 10)+
geom_vline(xintercept = 5.5, colour = "black", size = 1)+
facet_grid(OTU~.)+
geom_hline(yintercept=c(1.96,-1.96), linetype = "dashed", colour = "gray22")+
scale_x_discrete( limits=c("NM1","NM2","NM3", "NM4", "NM5", "Green", "Pink", "Brown", "S1", "S2"))+
scale_y_continuous( limits=c(-5,5))+
opts(
title="Cyanobacteria \n Young Mat Old Mat",
panel.background = theme_rect(linetype = "solid", size = 2),
panel.grid.major = theme_blank(),
panel.grid.minor = theme_blank(),
axis.ticks = theme_blank()
)+
geom_point(aes(size = ntaxa,colour = type))+
scale_colour_manual(values=c("dodgerblue4", "firebrick"))+
geom_line(aes(layer, cyanos$z[1:48], group=age), lwd = 0.5, col = "firebrick")+
geom_line(aes(layer, cyanos$z[49:96], group=age), lwd = 0.5, col = "dodgerblue4")+
labs(colour = "Metric", size = "OTU Richness", y = "Z-statistic", x = "Layer")
cyplot
Raw
gistfile1.txt
"age" "layer" "ntaxa" "z" "type" "group" "OTU"
"old" "Brown" 49 -0.4963348529 "mpd" "PSB" 97
"NA" "G1" 33 -0.2951470052 "mpd" "PSB" 97
"NA" "G2" 6 0.8450593798 "mpd" "PSB" 97
"old" "Green" 37 0.2691702206 "mpd" "PSB" 97
"young" "NM1" 14 -1.6164228931 "mpd" "PSB" 97
"young" "NM2" 26 0.4740739272 "mpd" "PSB" 97
"young" "NM3" 20 -0.8159880535 "mpd" "PSB" 97
"young" "NM4" 15 0.0021269779 "mpd" "PSB" 97
"young" "NM5" 12 -0.0276365806 "mpd" "PSB" 97
"old" "Pink" 64 -1.349143476 "mpd" "PSB" 97
"old" "S1" 21 -1.158061556 "mpd" "PSB" 97
"old" "S2" 11 -0.7156396595 "mpd" "PSB" 97
"old" "Brown" 71 0.5254403327 "mpd" "PSB" 93
"NA" "G1" 44 -1.0529956151 "mpd" "PSB" 93
"NA" "G2" 9 -2.3208668067 "mpd" "PSB" 93
"old" "Green" 45 -3.0404341848 "mpd" "PSB" 93
"young" "NM1" 12 -2.6708014636 "mpd" "PSB" 93
"young" "NM2" 56 -2.773076207 "mpd" "PSB" 93
"young" "NM3" 42 -2.8616551054 "mpd" "PSB" 93
"young" "NM4" 21 -1.2119401989 "mpd" "PSB" 93
"young" "NM5" 26 -2.6266690459 "mpd" "PSB" 93
"old" "Pink" 94 -0.5101405087 "mpd" "PSB" 93
"old" "S1" 39 -1.9708291881 "mpd" "PSB" 93
"old" "S2" 16 -0.8528266581 "mpd" "PSB" 93
"old" "Brown" 51 0.5107462699 "mpd" "PSB" 90
"NA" "G1" 45 -2.4225515142 "mpd" "PSB" 90
"NA" "G2" 7 0.754259578 "mpd" "PSB" 90
"old" "Green" 33 -1.0587972321 "mpd" "PSB" 90
"young" "NM1" 14 0.1423129439 "mpd" "PSB" 90
"young" "NM2" 34 -2.502069304 "mpd" "PSB" 90
"young" "NM3" 28 -2.2073212925 "mpd" "PSB" 90
"young" "NM4" 19 -1.3027164914 "mpd" "PSB" 90
"young" "NM5" 14 -0.6508750394 "mpd" "PSB" 90
"old" "Pink" 67 -0.2890493316 "mpd" "PSB" 90
"old" "S1" 31 -1.1607187915 "mpd" "PSB" 90
"old" "S2" 17 -0.7591819168 "mpd" "PSB" 90
"old" "Brown" 19 0.0230788105 "mpd" "PSB" 85
"NA" "G1" 11 -2.0207145034 "mpd" "PSB" 85
"NA" "G2" 5 0.2540042712 "mpd" "PSB" 85
"old" "Green" 6 -0.2193601531 "mpd" "PSB" 85
"young" "NM1" 6 -1.262318256 "mpd" "PSB" 85
"young" "NM2" 8 -1.6973492793 "mpd" "PSB" 85
"young" "NM3" 8 -0.9450700215 "mpd" "PSB" 85
"young" "NM4" 12 -0.3083151676 "mpd" "PSB" 85
"young" "NM5" 9 -1.4899725271 "mpd" "PSB" 85
"old" "Pink" 20 -2.77624444 "mpd" "PSB" 85
"old" "S1" 16 0.7683886159 "mpd" "PSB" 85
"old" "S2" 6 -1.715059401 "mpd" "PSB" 85
"old" "Brown" 11 -1.3730570499 "mpd" "cyano" 97
"NA" "G1" 179 -1.4206707804 "mpd" "cyano" 97
"NA" "G2" 224 1.7871124686 "mpd" "cyano" 97
"old" "Green" 182 -3.2394579869 "mpd" "cyano" 97
"young" "NM1" 242 -4.4882067963 "mpd" "cyano" 97
"young" "NM2" 154 2.572466239 "mpd" "cyano" 97
"young" "NM3" 90 2.233038625 "mpd" "cyano" 97
"young" "NM4" 25 0.3058317499 "mpd" "cyano" 97
"young" "NM5" 28 0.3545642451 "mpd" "cyano" 97
"old" "Pink" 32 -2.4629240375 "mpd" "cyano" 97
"old" "S1" 7 -1.1827596663 "mpd" "cyano" 97
"old" "S2" 0 "NA" "mpd" "cyano" 97
"old" "Brown" 17 -1.8658033284 "mpd" "cyano" 93
"NA" "G1" 174 -1.5380710566 "mpd" "cyano" 93
"NA" "G2" 199 0.5813909245 "mpd" "cyano" 93
"old" "Green" 168 -0.7030435249 "mpd" "cyano" 93
"young" "NM1" 190 -0.8183012311 "mpd" "cyano" 93
"young" "NM2" 154 -2.6552220369 "mpd" "cyano" 93
"young" "NM3" 123 -2.5782246159 "mpd" "cyano" 93
"young" "NM4" 30 -1.7893132707 "mpd" "cyano" 93
"young" "NM5" 48 -1.9858596615 "mpd" "cyano" 93
"old" "Pink" 46 -2.3319127735 "mpd" "cyano" 93
"old" "S1" 10 -1.2458289653 "mpd" "cyano" 93
"old" "S2" 2 0.3390424411 "mpd" "cyano" 93
"old" "Brown" 11 -1.4438100755 "mpd" "cyano" 90
"NA" "G1" 117 -1.3303807662 "mpd" "cyano" 90
"NA" "G2" 109 -0.1420634961 "mpd" "cyano" 90
"old" "Green" 101 -1.8844868088 "mpd" "cyano" 90
"young" "NM1" 121 -0.5615461038 "mpd" "cyano" 90
"young" "NM2" 102 0.701597309 "mpd" "cyano" 90
"young" "NM3" 91 -0.7581391812 "mpd" "cyano" 90
"young" "NM4" 32 -1.6217587048 "mpd" "cyano" 90
"young" "NM5" 34 -2.0708685477 "mpd" "cyano" 90
"old" "Pink" 38 -1.5266120023 "mpd" "cyano" 90
"old" "S1" 14 -1.4291462049 "mpd" "cyano" 90
"old" "S2" 2 -1.0322280257 "mpd" "cyano" 90
"old" "Brown" 16 -1.5672257093 "mpd" "cyano" 85
"NA" "G1" 38 -2.152305166 "mpd" "cyano" 85
"NA" "G2" 31 -1.2959129231 "mpd" "cyano" 85
"old" "Green" 32 -3.8965201561 "mpd" "cyano" 85
"young" "NM1" 33 -0.5958924264 "mpd" "cyano" 85
"young" "NM2" 30 -2.7556041279 "mpd" "cyano" 85
"young" "NM3" 33 -0.6266076083 "mpd" "cyano" 85
"young" "NM4" 24 -2.1425850098 "mpd" "cyano" 85
"young" "NM5" 20 -2.5568385175 "mpd" "cyano" 85
"old" "Pink" 23 -2.0821320209 "mpd" "cyano" 85
"old" "S1" 11 -1.191664414 "mpd" "cyano" 85
"old" "S2" 3 0.8560788138 "mpd" "cyano" 85
"old" "Brown" 5 -1.1087075275 "mpd" "clost" 85
"NA" "G1" 7 -1.5922792177 "mpd" "clost" 85
"NA" "G2" 0 "NA" "mpd" "clost" 85
"old" "Green" 1 "NA" "mpd" "clost" 85
"young" "NM1" 2 -0.980961702 "mpd" "clost" 85
"young" "NM2" 5 -1.6394412662 "mpd" "clost" 85
"young" "NM3" 6 1.0853750975 "mpd" "clost" 85
"young" "NM4" 5 -0.8493098813 "mpd" "clost" 85
"young" "NM5" 6 -0.0057310875 "mpd" "clost" 85
"old" "Pink" 6 0.3982229196 "mpd" "clost" 85
"old" "S1" 7 -1.6249730791 "mpd" "clost" 85
"old" "S2" 5 -1.0116088107 "mpd" "clost" 85
"old" "Brown" 9 -1.7718413457 "mpd" "clost" 90
"NA" "G1" 8 -0.5817689134 "mpd" "clost" 90
"NA" "G2" 0 "NA" "mpd" "clost" 90
"old" "Green" 0 "NA" "mpd" "clost" 90
"young" "NM1" 0 "NA" "mpd" "clost" 90
"young" "NM2" 3 0.5806546509 "mpd" "clost" 90
"young" "NM3" 1 "NA" "mpd" "clost" 90
"young" "NM4" 4 -1.398665782 "mpd" "clost" 90
"young" "NM5" 1 "NA" "mpd" "clost" 90
"old" "Pink" 5 1.409070296 "mpd" "clost" 90
"old" "S1" 16 -1.4346971464 "mpd" "clost" 90
"old" "S2" 8 -2.1254696646 "mpd" "clost" 90
"old" "Brown" 7 -0.0911344971 "mpd" "clost" 93
"NA" "G1" 4 -0.4499534144 "mpd" "clost" 93
"NA" "G2" 0 "NA" "mpd" "clost" 93
"old" "Green" 0 "NA" "mpd" "clost" 93
"young" "NM1" 1 "NA" "mpd" "clost" 93
"young" "NM2" 5 1.258412812 "mpd" "clost" 93
"young" "NM3" 2 1.0602452636 "mpd" "clost" 93
"young" "NM4" 4 0.988200505 "mpd" "clost" 93
"young" "NM5" 2 0.7262527182 "mpd" "clost" 93
"old" "Pink" 4 -0.7659524083 "mpd" "clost" 93
"old" "S1" 13 -2.8190525049 "mpd" "clost" 93
"old" "S2" 7 -1.9883072962 "mpd" "clost" 93
"old" "Brown" 7 0.1041110884 "mpd" "clost" 97
"NA" "G1" 2 -0.8631969249 "mpd" "clost" 97
"NA" "G2" 0 "NA" "mpd" "clost" 97
"old" "Green" 0 "NA" "mpd" "clost" 97
"young" "NM1" 0 "NA" "mpd" "clost" 97
"young" "NM2" 1 "NA" "mpd" "clost" 97
"young" "NM3" 2 0.6670776375 "mpd" "clost" 97
"young" "NM4" 2 0.394397803 "mpd" "clost" 97
"young" "NM5" 2 1.0881552822 "mpd" "clost" 97
"old" "Pink" 5 0.8233745543 "mpd" "clost" 97
"old" "S1" 11 -1.4874913541 "mpd" "clost" 97
"old" "S2" 5 -0.8330165384 "mpd" "clost" 97
"old" "Brown" 49 -1.6428626034 "mntd" "PSB" 97
"NA" "G1" 33 -0.7960255378 "mntd" "PSB" 97
"NA" "G2" 6 0.5897110763 "mntd" "PSB" 97
"old" "Green" 37 0.4261286664 "mntd" "PSB" 97
"young" "NM1" 14 -1.5732738263 "mntd" "PSB" 97
"young" "NM2" 26 0.1192961799 "mntd" "PSB" 97
"young" "NM3" 20 -0.6928150405 "mntd" "PSB" 97
"young" "NM4" 15 0.0731955725 "mntd" "PSB" 97
"young" "NM5" 12 -0.1825258635 "mntd" "PSB" 97
"old" "Pink" 64 -2.6367180291 "mntd" "PSB" 97
"old" "S1" 21 -1.4057562196 "mntd" "PSB" 97
"old" "S2" 11 -0.6149465221 "mntd" "PSB" 97
"old" "Brown" 71 -0.2389273989 "mntd" "PSB" 93
"NA" "G1" 44 -2.6600652077 "mntd" "PSB" 93
"NA" "G2" 9 -1.4470926227 "mntd" "PSB" 93
"old" "Green" 45 -1.9927358463 "mntd" "PSB" 93
"young" "NM1" 12 -1.1302795163 "mntd" "PSB" 93
"young" "NM2" 56 -2.0108377415 "mntd" "PSB" 93
"young" "NM3" 42 -2.4035830271 "mntd" "PSB" 93
"young" "NM4" 21 -1.5647880109 "mntd" "PSB" 93
"young" "NM5" 26 -1.2806316156 "mntd" "PSB" 93
"old" "Pink" 94 -0.8452762356 "mntd" "PSB" 93
"old" "S1" 39 -1.678258399 "mntd" "PSB" 93
"old" "S2" 16 -1.0342030962 "mntd" "PSB" 93
"old" "Brown" 51 0.2872261858 "mntd" "PSB" 90
"NA" "G1" 45 -1.5206450238 "mntd" "PSB" 90
"NA" "G2" 7 0.3870575368 "mntd" "PSB" 90
"old" "Green" 33 0.0553107079 "mntd" "PSB" 90
"young" "NM1" 14 0.8025036927 "mntd" "PSB" 90
"young" "NM2" 34 -1.1988949829 "mntd" "PSB" 90
"young" "NM3" 28 -1.4962830978 "mntd" "PSB" 90
"young" "NM4" 19 -0.4232400442 "mntd" "PSB" 90
"young" "NM5" 14 0.3174149145 "mntd" "PSB" 90
"old" "Pink" 67 -0.4341929059 "mntd" "PSB" 90
"old" "S1" 31 -0.9768125311 "mntd" "PSB" 90
"old" "S2" 17 -1.2620554074 "mntd" "PSB" 90
"old" "Brown" 19 0.0130230796 "mntd" "PSB" 85
"NA" "G1" 11 -1.6674590554 "mntd" "PSB" 85
"NA" "G2" 5 0.3376354213 "mntd" "PSB" 85
"old" "Green" 6 -0.0528659237 "mntd" "PSB" 85
"young" "NM1" 6 -0.884930047 "mntd" "PSB" 85
"young" "NM2" 8 -1.2305029767 "mntd" "PSB" 85
"young" "NM3" 8 -0.6608329063 "mntd" "PSB" 85
"young" "NM4" 12 -0.4935397762 "mntd" "PSB" 85
"young" "NM5" 9 -1.2657272277 "mntd" "PSB" 85
"old" "Pink" 20 -2.5250936743 "mntd" "PSB" 85
"old" "S1" 16 0.3429160692 "mntd" "PSB" 85
"old" "S2" 6 -1.418889772 "mntd" "PSB" 85
"old" "Brown" 11 -0.2483892119 "mntd" "cyano" 97
"NA" "G1" 179 0.6949209304 "mntd" "cyano" 97
"NA" "G2" 224 -2.0156150358 "mntd" "cyano" 97
"old" "Green" 182 -3.9927396153 "mntd" "cyano" 97
"young" "NM1" 242 -3.0116975901 "mntd" "cyano" 97
"young" "NM2" 154 0.6661800693 "mntd" "cyano" 97
"young" "NM3" 90 1.9521363422 "mntd" "cyano" 97
"young" "NM4" 25 -0.7913397853 "mntd" "cyano" 97
"young" "NM5" 28 -0.6681492701 "mntd" "cyano" 97
"old" "Pink" 32 -1.0577556627 "mntd" "cyano" 97
"old" "S1" 7 -0.3505972059 "mntd" "cyano" 97
"old" "S2" 0 "NA" "mntd" "cyano" 97
"old" "Brown" 17 -0.9437008359 "mntd" "cyano" 93
"NA" "G1" 174 -1.8523947593 "mntd" "cyano" 93
"NA" "G2" 199 -0.2705075783 "mntd" "cyano" 93
"old" "Green" 168 -2.6973270222 "mntd" "cyano" 93
"young" "NM1" 190 -2.3467978363 "mntd" "cyano" 93
"young" "NM2" 154 -2.0037833159 "mntd" "cyano" 93
"young" "NM3" 123 -1.6216701394 "mntd" "cyano" 93
"young" "NM4" 30 -1.9286272074 "mntd" "cyano" 93
"young" "NM5" 48 -2.0545862559 "mntd" "cyano" 93
"old" "Pink" 46 -1.6920589846 "mntd" "cyano" 93
"old" "S1" 10 -1.1422278049 "mntd" "cyano" 93
"old" "S2" 2 0.2845258207 "mntd" "cyano" 93
"old" "Brown" 11 -1.5079555958 "mntd" "cyano" 90
"NA" "G1" 117 -2.1351948147 "mntd" "cyano" 90
"NA" "G2" 109 -1.4950780687 "mntd" "cyano" 90
"old" "Green" 101 -2.4003928368 "mntd" "cyano" 90
"young" "NM1" 121 -1.7199737332 "mntd" "cyano" 90
"young" "NM2" 102 0.2115470509 "mntd" "cyano" 90
"young" "NM3" 91 -1.0194611288 "mntd" "cyano" 90
"young" "NM4" 32 -1.8526533899 "mntd" "cyano" 90
"young" "NM5" 34 -2.3517140605 "mntd" "cyano" 90
"old" "Pink" 38 -1.6809663579 "mntd" "cyano" 90
"old" "S1" 14 -1.4085846589 "mntd" "cyano" 90
"old" "S2" 2 -1.0273507724 "mntd" "cyano" 90
"old" "Brown" 16 -1.2381428386 "mntd" "cyano" 85
"NA" "G1" 38 -2.1258402353 "mntd" "cyano" 85
"NA" "G2" 31 -1.4672507456 "mntd" "cyano" 85
"old" "Green" 32 -1.5626524819 "mntd" "cyano" 85
"young" "NM1" 33 -2.440681021 "mntd" "cyano" 85
"young" "NM2" 30 -2.223379065 "mntd" "cyano" 85
"young" "NM3" 33 -0.2656307213 "mntd" "cyano" 85
"young" "NM4" 24 1.0480508445 "mntd" "cyano" 85
"young" "NM5" 20 -1.5812583697 "mntd" "cyano" 85
"old" "Pink" 23 -2.9310654471 "mntd" "cyano" 85
"old" "S1" 11 -0.9563364533 "mntd" "cyano" 85
"old" "S2" 3 0.1461179315 "mntd" "cyano" 85
"old" "Brown" 5 -1.0339060701 "mntd" "clost" 85
"NA" "G1" 7 -2.1366113202 "mntd" "clost" 85
"NA" "G2" 0 "NA" "mntd" "clost" 85
"old" "Green" 1 "NA" "mntd" "clost" 85
"young" "NM1" 2 -1.0299133733 "mntd" "clost" 85
"young" "NM2" 5 -1.4831251635 "mntd" "clost" 85
"young" "NM3" 6 0.8601456427 "mntd" "clost" 85
"young" "NM4" 5 -1.335786109 "mntd" "clost" 85
"young" "NM5" 6 -0.2956631196 "mntd" "clost" 85
"old" "Pink" 6 -0.3928060245 "mntd" "clost" 85
"old" "S1" 7 -2.0714796382 "mntd" "clost" 85
"old" "S2" 5 -0.8427135748 "mntd" "clost" 85
"old" "Brown" 9 -0.8415821696 "mntd" "clost" 90
"NA" "G1" 8 -1.4815034609 "mntd" "clost" 90
"NA" "G2" 0 "NA" "mntd" "clost" 90
"old" "Green" 0 "NA" "mntd" "clost" 90
"young" "NM1" 0 "NA" "mntd" "clost" 90
"young" "NM2" 3 0.0505025993 "mntd" "clost" 90
"young" "NM3" 1 "NA" "mntd" "clost" 90
"young" "NM4" 4 -1.4919483107 "mntd" "clost" 90
"young" "NM5" 1 "NA" "mntd" "clost" 90
"old" "Pink" 5 1.0462377892 "mntd" "clost" 90
"old" "S1" 16 -1.1886727585 "mntd" "clost" 90
"old" "S2" 8 -1.4169880673 "mntd" "clost" 90
"old" "Brown" 7 -0.2589898422 "mntd" "clost" 93
"NA" "G1" 4 -0.5955880171 "mntd" "clost" 93
"NA" "G2" 0 "NA" "mntd" "clost" 93
"old" "Green" 0 "NA" "mntd" "clost" 93
"young" "NM1" 1 "NA" "mntd" "clost" 93
"young" "NM2" 5 0.305482819 "mntd" "clost" 93
"young" "NM3" 2 1.0645157281 "mntd" "clost" 93
"young" "NM4" 4 0.3424569581 "mntd" "clost" 93
"young" "NM5" 2 0.7536445642 "mntd" "clost" 93
"old" "Pink" 4 -0.7387324089 "mntd" "clost" 93
"old" "S1" 13 -0.6157567322 "mntd" "clost" 93
"old" "S2" 7 -0.2167288494 "mntd" "clost" 93
"old" "Brown" 7 -0.476829507 "mntd" "clost" 97
"NA" "G1" 2 -0.8606290055 "mntd" "clost" 97
"NA" "G2" 0 "NA" "mntd" "clost" 97
"old" "Green" 0 "NA" "mntd" "clost" 97
"young" "NM1" 0 "NA" "mntd" "clost" 97
"young" "NM2" 1 "NA" "mntd" "clost" 97
"young" "NM3" 2 0.6950961697 "mntd" "clost" 97
"young" "NM4" 2 0.3835257792 "mntd" "clost" 97
"young" "NM5" 2 1.0619063802 "mntd" "clost" 97
"old" "Pink" 5 0.5132235793 "mntd" "clost" 97
"old" "S1" 11 -1.0372720972 "mntd" "clost" 97
"old" "S2" 5 -0.188553129 "mntd" "clost" 97
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