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Metatranscriptomics heatmap and stacked bar plot visualization

Binder DOI

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

Links