phytoclass-shiny-gui

GUI built using R.shiny for CHEMTAX and phytoclass users.

TODO:

• add options to clustering
  • distanceType (manhattan etc)

Setup

ubuntu

sudo apt install libfribidi-dev libfontconfig1-dev libfontconfig1-dev

all

if (!require('devtools')) install.packages("devtools")
devtools::install_local()

• global.R: data prep and library loading
• ui.R: user interface
• server.R: server functions

quartoReport module

The quartoReport module provides a shiny setup for rendering quarto documents within a shiny server using configurable inputs and downloadable outputs.

graph TD

fileUpload{{File Upload}}

subgraph user files
  pigmentsUserFile[["pigments.csv"]]
  taxaUserFile[["taxa.csv"]]
end

subgraph R environment
  initRDS["inital env RDS"]
  clusterRDSPath["cluster RDS path"]
end

subgraph server files
  pigmentsFile["pigments_{hash}.csv"]
  taxaFile["taxa_{hash}.csv"]
  clusterRDS[["cluster.rds"]]
  annealRDS[["anneal.rds"]]
end

pigmentsUserFile --> fileUpload 
    fileUpload --> pigmentsFile
    fileUpload --> initRDS
taxaUserFile --> fileUpload 
    fileUpload --> taxaFile


pigmentsFile --> cluster{{cluster}} --> clusterRDS

anneal{{anneal}}

clusterRDSPath --> anneal
clusterRDS --> anneal --> annealRDS

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.qmd reports

.qmd reports used are stored in ./app/www/.

functional overview

1. define input

• upload .rds
• (NYI) html to set up the input
• (NYI)R code to set up variables

2. generate the report with given input
3. download

• (NYI) .rds of the final environment
• (NYI) .qmd of the report (including variable setup at beggining)
• (NYI) .pdf of the report

reports info flow

Generalized info flow for quartoReport module:

graph TD

contextBuilder{{buildContext}}
contextLoader{{loadContext}}
quartoRender{{renderReport}}

subgraph user files
  userContextFile[["contextFile.rds"]]
  userDataFile[["dataFile.csv"]]
end

subgraph context settings GUI
  settingsText[["settings textbox"]]
  contextUploader[["Context Uploader"]]
  fileUploader[["Data File Uploader"]]
end

userDataFile --> fileUploader --> contextBuilder
userContextFile --> contextUploader --> contextBuilder
settingsText --> contextBuilder

subgraph R rendering environment
  quartoParams["quarto params"]
end

subgraph server files
  preRenderContext["preRenderContext_{hash}.rds"]
  postRenderContext[["postRenderContext_{hash}.rds"]]
  report[["report.md"]]
end

contextBuilder --> preRenderContext

preRenderContext --> contextLoader --> quartoParams

quartoParams --> 
  quartoRender --> postRenderContext
  quartoRender --> report

report --> downloadReport{{"Download Report"}} 
  downloadReport --> reportmd[["report.md"]]
  downloadReport --> reportpdf[["report.pdf"]]

downloadContext{{"Download Context"}}
postRenderContext --> downloadContext
preRenderContext --> downloadContext

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