Tips: Pavian Load Large Data

omicx.cc
Software, NGS
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Pavian is a interactive browser application for analyzing and visualization metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Here are a few tips for Pavian to work with large data.

1. Error: Maximum upload size exceeded

E.g., Maximum upload 50M files for Pavian, simple input:

pavian::runApp(port=5000, maxUploadSize=50*1024^2)

# Or
pavian::runApp(port=5000, maxUploadSize="50M")
  • Besides M (megabyte), B (byte), K (kilobyte) and G (gigabyte) also supported.
  • This option is defined in the script runApp.R in Pavian source.

2. Can’t upload more than 99 samples at a time

Clone the Pavian repository locally

git clone https://github.com/fbreitwieser/pavian.git

Edit pavian/R/datainput-read_server_directory.R:

vi pavian/R/datainput-read_server_directory.R

In line 72, modify pavian.maxFiles from 100 to 1000.

Then start R

R

Next install modified repository as Pavian and run the shiny app:

library(devtools)
install("./pavian")
pavian::runApp(port=5000)

A. Reference

  1. https://github.com/fbreitwieser/pavian
  2. https://github.com/fbreitwieser/pavian/issues/23
  3. https://github.com/fbreitwieser/pavian/issues/63