plotPD: Plot Faith's PD
In jeffkimbrel/jakR: jakR Miscellaneous Scripts
plotPD R Documentation
Plot Faith's PD
Description
This function iteratively removes the least abundant sequence in a phyloseq sample, re-roots the tree, calculates Faith's PD, and plots the results.
Returns a list with a dataframe (results$df) and two different plots.
Usage
plotPD(phyloObject)
Details
results$p1 is from iteratively removing the lowest abundance sequences per sample. This is done on a per sample basis - if
a sequence is lowest in sample A but not sample B, it is removed from sample A but retained in sample B until it is lowest there.
If there are multiple sequences tied for lowest in a sample, they are all removed at once - hence there can be jumps along the x axis.
results$p2 uses the same data and criteria as results$p1, except now the x axis is the sequence count when removed. An X value of 10 for example
means that is the PD with all sequences of abundance 10 or less removed.
jeffkimbrel/jakR documentation built on April 6, 2024, 8:48 p.m.
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| plotPD | R Documentation |
Plot Faith's PD
Description
This function iteratively removes the least abundant sequence in a phyloseq sample, re-roots the tree, calculates Faith's PD, and plots the results. Returns a list with a dataframe (results$df) and two different plots.
Usage
plotPD(phyloObject)
Details
results$p1 is from iteratively removing the lowest abundance sequences per sample. This is done on a per sample basis - if a sequence is lowest in sample A but not sample B, it is removed from sample A but retained in sample B until it is lowest there. If there are multiple sequences tied for lowest in a sample, they are all removed at once - hence there can be jumps along the x axis.
results$p2 uses the same data and criteria as results$p1, except now the x axis is the sequence count when removed. An X value of 10 for example means that is the PD with all sequences of abundance 10 or less removed.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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