SRM data - quantifying tech. rep. quality

Today I figured out how to calculate distances between tech reps on the NMDS plot to numerically validate my removal of poor-quality reps. I ended up removing a few more reps (as compared to visually inspecting reps), but as a whole not much has changed. I also generated a couple plots using Plotly, which is fantastic. Plotly creates interactive plots so you can hover over points, zoom into a plot, etc.

Here is a plot of my technical replicate NMDS:

tech rep

If you download this file and drag into your browser you can view it in Plotly: tech rep plotly (couldn’t quickly figure out how to render Plotly in my notebook; if you know how please let me know in comments!)

R script written to calculate euclidian distances between technical replicates on NMDS & plot via Plotly:

#### Calculate distances between tech rep points on NMDS plot and plot to ID technical rep outliers
library(reshape2) <- NULL
for(i in 1:length(SRMsamples)) {
  G <- SRMsamples[i]
  D <- dist(SRM.nmds.samples.sorted[grepl(G, rownames(SRM.nmds.samples.sorted)),], method="euclidian") 
  M <- melt(as.matrix(D), varnames = c("row", "col")) <- rbind(, M)
} <-[!$value == 0,] #remove rows with value=0 (distance between same points)[,1:2] <- apply([,1:2], 2, function(y) gsub('G|G0|G00', '', y)) #remove extraneous "G00" from point names
p1 <- plot_ly(, y=~value, type="scatter", mode="text", text=~row)
htmlwidgets::saveWidget(as_widget(p1), "NMDS-technical-replicate-distances.html")
summary($value) <-[$value>.2,] #which tech rep distances are >0.2

Resulting “” were determined as distances >0.2 on NMDS plot/scale. This standard is still not good enough for publication; need to investigate NMDS stats to see if there is a sd, variance, or something that I can use to validate my 0.2 selection.
bad tech reps combinations >0.2

Plot of technical rep distances using Plotly: tech rep distances plotly

Written on October 15, 2017