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Taxa and Function Summary

GitHub repository: speeding-up-science-workshops/MetaT-taxa-and-function-summary/

DOI: 10.5281/zenodo.3519414

Binder

Summary

Visualization codes from the first "speeding up science workshop". This repository contains codes to make heatmap and stacked bar plots for metatranscriptomic function and RNA-based taxonomy summaries. The demonstration shown here is using data from this paper by Michael D. Lee.

Quick Start

  • Once the Binder is started, user will enter a virtual Rstudio interface.
  • User can either excute the codes with included samples by clicking on the "function-summary.Rmd" and "taxa-summary.rmd" scripts or upload new data files by clicking the Upload button at the lower right panel.
  • To save a rendered html output, user can click the knitr button at the upper left panel.

Example Input

1. A count table with either gene or taxonomy profile per sample.

If the user want to normalize the count table, the "raw-to-TPM-conversion.R" script is included in this Binder to perform such task.

CDS_ID Low_A Low_B High_A High_B
1 CDS_100 10.980509 8.364332 28.15585 0.000000
2 CDS_10011 2.284764 1.522854 10.25240 0.000000
3 CDS_10013 9.833839 6.554506 0.00000 0.000000
4 CDS_10015 7.194288 2.501831 0.00000 0.000000
5 CDS_10016 0.000000 0.000000 44.98916 0.000000

2. A taxonomy or KEGG annotation table.

CDS_ID Domain Phylum Class Order Family Genus Species
1 CDS_2383 Archaea Euryarchaeota Methanococci Methanococcales Methanocaldococcaceae Methanocaldococcus Methanocaldococcus_infernus
2 CDS_4184 Archaea Euryarchaeota Methanomicrobia Methanosarcinales Methanosarcinaceae Methanosarcina Methanosarcina_barkeri
3 CDS_6601 Archaea Euryarchaeota Methanomicrobia Methanosarcinales Methanosarcinaceae Methanosarcina Methanosarcina_barkeri
4 CDS_6904 Archaea Euryarchaeota Methanococci Methanococcales Methanococcaceae Methanococcus Methanococcus_vannielii
5 CDS_7927 Archaea Euryarchaeota Halobacteria Natrialbales Natrialbaceae Haloterrigena Haloterrigena_jeotgali

3. A sample metainfo table

SampleID Place Group
1 High_A High A
2 High_B High B
3 Low_A Low A
4 Low_B Low B

Example Output

  • Thumbnail of expected Heatmap

  • Thumbnail of expected bar plot

Author