I want to map the posterior probability values to the nodes of the phylogenetic tree using ggtree. The the output is a nexus file (.tre) format from mrbayes the following command was used
p <- ggtree(t1, branch.length="none", layout = "rectangular")
p +
geom_tiplab(aes(label = label), size = 3, color = "steelblue", hjust = -0.1)+
geom_hilight(node=20, fill="gold") +
geom_hilight(node=16, fill="purple")+
geom_text2(aes(label = prob), size = 1)
I am getting the following error
Error in geom_text2():
! Problem while computing aesthetics.
ℹ Error occurred in the 6th layer.
Caused by error:
! object 'prob' not found.
While my nexus file have the prob mentioned, the following is the section of the file
#NEXUS
[ID: 8306796616]
begin taxa;
dimensions ntax=12;
taxlabels
Tarsius_syrichta
Lemur_catta
Homo_sapiens
Pan
Gorilla
Pongo
Hylobates
Macaca_fuscata
M_mulatta
M_fascicularis
M_sylvanus
Saimiri_sciureus
;
end;
begin trees;
translate
1 Tarsius_syrichta,
2 Lemur_catta,
3 Homo_sapiens,
4 Pan,
5 Gorilla,
6 Pongo,
7 Hylobates,
8 Macaca_fuscata,
9 M_mulatta,
10 M_fascicularis,
11 M_sylvanus,
12 Saimiri_sciureus
;
tree con_50_majrule = [&U] (1[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:5.485518e-001[&length_mean=5.56956779e-001,length_median=5.48551800e-001,length_95%HPD={3.77505700e-001,7.37138400e-001}],2[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:3.758621e-001[&length_mean=3.82169520e-001,length_median=3.75862100e-001,length_95%HPD={2.41146600e-001,5.42920800e-001}],((((((3[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:5.173710e-002[&length_mean=5.23927216e-002,length_median=5.17371000e-002,length_95%HPD={3.01313000e-002,7.47395300e-002}],4[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:6.266943e-002[&length_mean=6.38756412e-002,length_median=6.26694300e-002,length_95%HPD={3.74561800e-002,8.71595900e-002}])[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:3.108751e-002[&length_mean=3.19526940e-002,length_median=3.10875100e-002,length_95%HPD={1.02709000e-002,5.57957100e-002}],5[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:6.003833e-002[&length_mean=6.06377255e-002,length_median=6.00383300e-002,length_95%HPD={3.16122100e-002,9.10847500e-002}])[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:8.866484e-002[&length_mean=9.13447623e-002,length_median=8.86648400e-002,length_95%HPD={4.73526800e-002,1.37318800e-001}],6[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:1.589201e-001[&length_mean=1.61158193e-001,length_median=1.58920100e-001,length_95%HPD={1.11871000e-001,2.20607400e-001}])[prob=9.98002663e-001,prob_stddev=9.41553637e-004,prob_range={9.97336884e-001,9.98668442e-001},prob(percent)="100",prob+-sd="100+-0"]:5.972794e-002[&length_mean=6.20651005e-002,length_median=5.97279400e-002,length_95%HPD={2.13975900e-002,1.12735000e-001}],7[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:1.818819e-001[&length_mean=1.85069215e-001,length_median=1.81881900e-001,length_95%HPD={1.17014400e-001,2.52948800e-001}])[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:1.381715e-001[&length_mean=1.41605087e-001,length_median=1.38171500e-001,length_95%HPD={6.54783600e-002,2.19092100e-001}],(((8[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:1.737566e-002[&length_mean=1.77030261e-002,length_median=1.73756600e-002,length_95%HPD={6.36735700e-003,2.99884700e-002}],9[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:2.333494e-002[&length_mean=2.37074923e-002,length_median=2.33349400e-002,length_95%HPD={1.09116200e-002,3.65187800e-002}])[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:3.551152e-002[&length_mean=3.62366830e-002,length_median=3.55115200e-002,length_95%HPD={1.73814900e-002,5.76692900e-002}],10[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:5.814620e-002[&length_mean=5.91708419e-002,length_median=5.81462000e-002,length_95%HPD={3.57017600e-002,8.45987900e-002}])[prob=9.96671105e-001,prob_stddev=9.41553637e-004,prob_range={9.96005326e-001,9.97336884e-001},prob(percent)="100",prob+-sd="100+-0"]:4.640086e-002[&length_mean=4.87692857e-002,length_median=4.64008600e-002,length_95%HPD={1.32313400e-002,8.72136000e-002}],11[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:7.647351e-002[&length_mean=7.66834711e-002,length_median=7.64735100e-002,length_95%HPD={3.48725000e-002,1.13763500e-001}])[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:2.818300e-001[&length_mean=2.86814156e-001,length_median=2.81830000e-001,length_95%HPD={1.90986800e-001,3.97046100e-001}])[prob=9.95339547e-001,prob_stddev=9.41553637e-004,prob_range={9.94673768e-001,9.96005326e-001},prob(percent)="100",prob+-sd="100+-0"]:1.326907e-001[&length_mean=1.37257161e-001,length_median=1.32690700e-001,length_95%HPD={3.73737300e-002,2.42976000e-001}],12[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:4.804155e-001[&length_mean=4.88972368e-001,length_median=4.80415500e-001,length_95%HPD={3.35837400e-001,6.63001600e-001}])[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:3.160860e-001[&length_mean=3.22154727e-001,length_median=3.16086000e-001,length_95%HPD={1.80630100e-001,4.72930900e-001}]);
end;
Thanking you
suji
I want to map the posterior probability values to the nodes of the phylogenetic tree using ggtree. The the output is a nexus file (.tre) format from mrbayes the following command was used
p <- ggtree(t1, branch.length="none", layout = "rectangular")
p +
geom_tiplab(aes(label = label), size = 3, color = "steelblue", hjust = -0.1)+
geom_hilight(node=20, fill="gold") +
geom_hilight(node=16, fill="purple")+
geom_text2(aes(label = prob), size = 1)
I am getting the following error
Error in
geom_text2():! Problem while computing aesthetics.
ℹ Error occurred in the 6th layer.
Caused by error:
! object 'prob' not found.
While my nexus file have the prob mentioned, the following is the section of the file
#NEXUS
[ID: 8306796616]
begin taxa;
dimensions ntax=12;
taxlabels
Tarsius_syrichta
Lemur_catta
Homo_sapiens
Pan
Gorilla
Pongo
Hylobates
Macaca_fuscata
M_mulatta
M_fascicularis
M_sylvanus
Saimiri_sciureus
;
end;
begin trees;
translate
1 Tarsius_syrichta,
2 Lemur_catta,
3 Homo_sapiens,
4 Pan,
5 Gorilla,
6 Pongo,
7 Hylobates,
8 Macaca_fuscata,
9 M_mulatta,
10 M_fascicularis,
11 M_sylvanus,
12 Saimiri_sciureus
;
tree con_50_majrule = [&U] (1[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:5.485518e-001[&length_mean=5.56956779e-001,length_median=5.48551800e-001,length_95%HPD={3.77505700e-001,7.37138400e-001}],2[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:3.758621e-001[&length_mean=3.82169520e-001,length_median=3.75862100e-001,length_95%HPD={2.41146600e-001,5.42920800e-001}],((((((3[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:5.173710e-002[&length_mean=5.23927216e-002,length_median=5.17371000e-002,length_95%HPD={3.01313000e-002,7.47395300e-002}],4[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:6.266943e-002[&length_mean=6.38756412e-002,length_median=6.26694300e-002,length_95%HPD={3.74561800e-002,8.71595900e-002}])[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:3.108751e-002[&length_mean=3.19526940e-002,length_median=3.10875100e-002,length_95%HPD={1.02709000e-002,5.57957100e-002}],5[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:6.003833e-002[&length_mean=6.06377255e-002,length_median=6.00383300e-002,length_95%HPD={3.16122100e-002,9.10847500e-002}])[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:8.866484e-002[&length_mean=9.13447623e-002,length_median=8.86648400e-002,length_95%HPD={4.73526800e-002,1.37318800e-001}],6[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:1.589201e-001[&length_mean=1.61158193e-001,length_median=1.58920100e-001,length_95%HPD={1.11871000e-001,2.20607400e-001}])[prob=9.98002663e-001,prob_stddev=9.41553637e-004,prob_range={9.97336884e-001,9.98668442e-001},prob(percent)="100",prob+-sd="100+-0"]:5.972794e-002[&length_mean=6.20651005e-002,length_median=5.97279400e-002,length_95%HPD={2.13975900e-002,1.12735000e-001}],7[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:1.818819e-001[&length_mean=1.85069215e-001,length_median=1.81881900e-001,length_95%HPD={1.17014400e-001,2.52948800e-001}])[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:1.381715e-001[&length_mean=1.41605087e-001,length_median=1.38171500e-001,length_95%HPD={6.54783600e-002,2.19092100e-001}],(((8[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:1.737566e-002[&length_mean=1.77030261e-002,length_median=1.73756600e-002,length_95%HPD={6.36735700e-003,2.99884700e-002}],9[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:2.333494e-002[&length_mean=2.37074923e-002,length_median=2.33349400e-002,length_95%HPD={1.09116200e-002,3.65187800e-002}])[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:3.551152e-002[&length_mean=3.62366830e-002,length_median=3.55115200e-002,length_95%HPD={1.73814900e-002,5.76692900e-002}],10[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:5.814620e-002[&length_mean=5.91708419e-002,length_median=5.81462000e-002,length_95%HPD={3.57017600e-002,8.45987900e-002}])[prob=9.96671105e-001,prob_stddev=9.41553637e-004,prob_range={9.96005326e-001,9.97336884e-001},prob(percent)="100",prob+-sd="100+-0"]:4.640086e-002[&length_mean=4.87692857e-002,length_median=4.64008600e-002,length_95%HPD={1.32313400e-002,8.72136000e-002}],11[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:7.647351e-002[&length_mean=7.66834711e-002,length_median=7.64735100e-002,length_95%HPD={3.48725000e-002,1.13763500e-001}])[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:2.818300e-001[&length_mean=2.86814156e-001,length_median=2.81830000e-001,length_95%HPD={1.90986800e-001,3.97046100e-001}])[prob=9.95339547e-001,prob_stddev=9.41553637e-004,prob_range={9.94673768e-001,9.96005326e-001},prob(percent)="100",prob+-sd="100+-0"]:1.326907e-001[&length_mean=1.37257161e-001,length_median=1.32690700e-001,length_95%HPD={3.73737300e-002,2.42976000e-001}],12[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:4.804155e-001[&length_mean=4.88972368e-001,length_median=4.80415500e-001,length_95%HPD={3.35837400e-001,6.63001600e-001}])[prob=1.00000000e+000,prob_stddev=0.00000000e+000,prob_range={1.00000000e+000,1.00000000e+000},prob(percent)="100",prob+-sd="100+-0"]:3.160860e-001[&length_mean=3.22154727e-001,length_median=3.16086000e-001,length_95%HPD={1.80630100e-001,4.72930900e-001}]);
end;
Thanking you
suji