Comments (4)
zkamvar
commented on June 26, 2024
If you would like to visualise the MLGs and their relationships across or between populations, you can use the mlg.table() function with the option color = TRUE (and/or background = TRUE if you want a separate plot for each population)
library(poppr)
#> Loading required package: adegenet
#> Loading required package: ade4
#>
#> /// adegenet 2.1.5 is loaded ////////////
#>
#> > overview: '?adegenet'
#> > tutorials/doc/questions: 'adegenetWeb()'
#> > bug reports/feature requests: adegenetIssues()
#> Registered S3 method overwritten by 'pegas':
#> method from
#> print.amova ade4
#> This is poppr version 2.9.3. To get started, type package?poppr
#> OMP parallel support: available
data(Aeut)
mlg.table(Aeut, plot = TRUE, color = TRUE)
#> MLG.1 MLG.2 MLG.3 MLG.4 MLG.5 MLG.6 MLG.7 MLG.8 MLG.9 MLG.10 MLG.11
#> Athena 1 0 0 0 0 0 1 1 1 1 1
#> Mt. Vernon 0 2 1 1 1 1 0 0 0 0 0
#> MLG.12 MLG.13 MLG.14 MLG.15 MLG.16 MLG.17 MLG.18 MLG.19 MLG.20
#> Athena 1 2 3 1 2 2 1 1 9
#> Mt. Vernon 0 0 0 0 0 0 0 0 0
#> MLG.21 MLG.22 MLG.23 MLG.24 MLG.25 MLG.26 MLG.27 MLG.28 MLG.29
#> Athena 1 1 2 2 1 1 1 1 1
#> Mt. Vernon 0 0 0 0 0 0 0 0 0
#> MLG.30 MLG.31 MLG.32 MLG.33 MLG.34 MLG.35 MLG.36 MLG.37 MLG.38
#> Athena 1 2 2 1 1 3 2 1 1
#> Mt. Vernon 0 0 0 0 0 0 0 0 0
#> MLG.39 MLG.40 MLG.41 MLG.42 MLG.43 MLG.44 MLG.45 MLG.46 MLG.47
#> Athena 1 1 1 1 1 1 1 1 1
#> Mt. Vernon 0 0 0 0 0 0 0 0 0
#> MLG.48 MLG.49 MLG.50 MLG.51 MLG.52 MLG.53 MLG.54 MLG.55 MLG.56
#> Athena 1 1 1 1 2 1 0 0 0
#> Mt. Vernon 0 0 0 0 0 0 1 1 1
#> MLG.57 MLG.58 MLG.59 MLG.60 MLG.61 MLG.62 MLG.63 MLG.64 MLG.65
#> Athena 1 0 1 2 1 1 2 1 1
#> Mt. Vernon 0 1 1 0 0 0 0 0 0
#> MLG.66 MLG.67 MLG.68 MLG.69 MLG.70 MLG.71 MLG.72 MLG.73 MLG.74
#> Athena 5 1 1 0 0 0 0 0 0
#> Mt. Vernon 0 0 0 4 5 1 2 1 3
#> MLG.75 MLG.76 MLG.77 MLG.78 MLG.79 MLG.80 MLG.81 MLG.82 MLG.83
#> Athena 0 0 0 0 0 0 0 0 0
#> Mt. Vernon 5 2 3 2 1 10 2 1 1
#> MLG.84 MLG.85 MLG.86 MLG.87 MLG.88 MLG.89 MLG.90 MLG.91 MLG.92
#> Athena 0 0 0 0 0 0 0 0 0
#> Mt. Vernon 1 1 1 2 2 1 2 2 1
#> MLG.93 MLG.94 MLG.95 MLG.96 MLG.97 MLG.98 MLG.99 MLG.100 MLG.101
#> Athena 1 1 0 0 0 0 0 0 0
#> Mt. Vernon 0 0 1 2 4 1 2 1 2
#> MLG.102 MLG.103 MLG.104 MLG.105 MLG.106 MLG.107 MLG.108 MLG.109
#> Athena 0 0 0 0 0 0 1 1
#> Mt. Vernon 1 2 1 1 1 1 0 0
#> MLG.110 MLG.111 MLG.112 MLG.113 MLG.114 MLG.115 MLG.116 MLG.117
#> Athena 1 1 1 1 1 0 0 0
#> Mt. Vernon 0 0 0 0 0 1 1 1
#> MLG.118 MLG.119
#> Athena 1 1
#> Mt. Vernon 0 0
Created on 2022-02-07 by the reprex package (v2.0.1)
Additionally, if you want to visualise the genetic relationships between the MLGs along with their population assignments, then you can create a minimum spanning network: https://grunwaldlab.github.io/Population_Genetics_in_R/Minimum_Spanning_Networks.html
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dionnecargy
commented on June 26, 2024
Hi, thank you for that explanation. I clarify, however, that I want to subset the data to only visualise MLG counts greater than or equal to 2.
i.e.:
Thanks.
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zkamvar
commented on June 26, 2024
Since mlg.id() will return a list with the IDs per MLG, you can use that list to subset your data by filtering on the length of the list item and then flattening that list with unlist()
library(poppr)
#> Loading required package: adegenet
#> Loading required package: ade4
#>
#> /// adegenet 2.1.5 is loaded ////////////
#>
#> > overview: '?adegenet'
#> > tutorials/doc/questions: 'adegenetWeb()'
#> > bug reports/feature requests: adegenetIssues()
#> Registered S3 method overwritten by 'pegas':
#> method from
#> print.amova ade4
#> This is poppr version 2.9.3. To get started, type package?poppr
#> OMP parallel support: available
data(Aeut)
ids <- mlg.id(Aeut)
only_clones <- unlist(ids[lengths(ids) > 1])
mlg.table(Aeut[only_clones], color = TRUE, plot = TRUE)
#> MLG.1 MLG.2 MLG.3 MLG.4 MLG.5 MLG.6 MLG.7 MLG.8 MLG.9 MLG.10 MLG.11
#> Athena 0 2 3 2 2 9 2 2 2 2 3
#> Mt. Vernon 2 0 0 0 0 0 0 0 0 0 0
#> MLG.12 MLG.13 MLG.14 MLG.15 MLG.16 MLG.17 MLG.18 MLG.19 MLG.20
#> Athena 2 2 1 2 2 5 0 0 0
#> Mt. Vernon 0 0 1 0 0 0 4 5 2
#> MLG.21 MLG.22 MLG.23 MLG.24 MLG.25 MLG.26 MLG.27 MLG.28 MLG.29
#> Athena 0 0 0 0 0 0 0 0 0
#> Mt. Vernon 3 5 2 3 2 10 2 2 2
#> MLG.30 MLG.31 MLG.32 MLG.33 MLG.34 MLG.35 MLG.36
#> Athena 0 0 0 0 0 0 0
#> Mt. Vernon 2 2 2 4 2 2 2
Created on 2022-02-08 by the reprex package (v2.0.1)
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dionnecargy
commented on June 26, 2024
Thank you so much! This works perfectly!
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