symbioR visualise sequences

symbioR includes a shiny app that can better visualise the ITS2 Symbiodinium community outputs from symportal. The shiny viewer allows:

• uploading sequences via “select folder” for simple use

• pplotly to interact with plots to reveal rare seqID types

• visualisation of relative vs absolute sequence abundances

• setting thresholds to remove rare sequences

• setting thresholds to “ghost” rare sequences and enhance visualisation

• filtering of plots by seqID

• filtering of plots by sample_name

• splitting large datasets across multiple rows

• ordering samples by hierarchical clustering of sequences (bray-curtis, jaccard, euclidian, hellinger)

• saving plots to png, jpg, pdf formats

library(tidyverse)
library(symbioR)


set.seed(1)

folder_path <- ("/symbiodinium/20230120T102936_esampayo")


view_sequences(folder_path)

Or call view_sequences() with an empty plot and upload the folder using the folder window:

library(tidyverse)
library(symbioR)


set.seed(1)

folder_path <- ("/symbiodinium/20230120T102936_esampayo")


view_sequences(folder_path)