Metatranscriptomics heatmap and stacked bar plot visualization

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 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

• Zhengyao "Zeya" Xue, Github ID @zeyaxue and ORCID

Links

• Zenodo Binder:
• Github Binder:
• Github Repository: https://github.com/zeyaxue/speeding-up-sci-heatmap-barplot