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Detection of growth- and metabolism-altering interactions within a defined microbiota

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asf_interactions's Issues

submit NMR spectra to MetaboLights

Add HPC code used for gapfilling

Clean up experimental condition labels in subplots of Figure 7D

Use full metabolite names

Port notebook for generating growth curves to repository

Move the optical density growth curve notebook and all associated data to this repository.

Use consistent statistical threshold value when graphically representing rejection of null hypothesis

Edit Figure 5

Rename CRAM to ConYE, and add descriptive column labels to indicate where the volcano plots are from, and that the middle column describes "actual behavior"

Finalize figure 1

Finalize figure 1 by cleaning up box scatters for overall abundance.

Clean PCA notebook

The analysis and figures are finished, but some commenting needs to be removed/improved and linting needs to be performed.

Overlay p-values on fig 1C, 1D

Add primer design scripts to this repository

Add the primer design scripts, and verify the location and identity of target genes.

Update readme with directory organization and file summaries

Replot qPCR figure with clip_on=False

Replot the qPCR figure with clop_on=False to get the entire symbol within each subplot frame for the monoculture abundance data.

Change all figure references to "strain" from "species"

Make this consistent with the text of the manuscript, where we refer to the ASF members as strains rather than species.

Set all plot fonts to Arial and increase font size to minimize manual changes

Generate volcano plots and summary metrics for CRAM model

Transfer over the plotting scripts for CRAM results into a new notebook and decide on which figures will go into figure 3 for the manuscript. Standardize the CRAM output and count metabolites categorically based on the monoculture differential abundance results (e.g. consumed by one species, produced by one species, etc.).

Transfer expectation model to this repository

Transfer the co-culture metabolome expectation model to this repository and decide on select figures to include for figure 3 in the manuscript.

GENRE-based inference on cross-feeding

Implement GENRE-based inference of cross-fed metabolites using our previously-generated ensembles. Use an ensemble of 100 GENREs for each species. Explore using micom rather than current scripts.

Add colorscale to abundance summary triangle plot

Determine normality and adjust tests as needed

Finalize normality tests and the corresponding downstream statistical test for DNA abundance and metabolite abundance.

Add final publication figures

Update the repository with vector art version of the final publication images.

Increase point size in Figure 4 and 6 volcano plots

Share axes on Fig 1B

For figure 1B (in vitro total growth by OD), share the Y axis so they can have a shared label to save space for manuscript.

Create an easy-to-use interface for ConYE so that users can test their own data

Add guide for "data parasites"

Add a folder with preprocessed, neatly organized data tables. Write a jupyter notebook guide to explain the data and simple ways to explore it/transform it.

increase dashed line thickness in figure 2

Add subpanel labels for A,B, and C in Figure 5

Each row should be labelled as a subpanel.

Edit Figure 4

Change references to "CRAM" to "ConYE"

Add detail to cartoon for clarity and guided interpretation based on potential observed and predicted outcomes

Rearrange labels on triangle key so that it doesn't seem as if the p value is directly derived from ConYE, rather ConYE is the system for generating expected values.

Fix Figure 4D typo

Figure 4D has ASF360 labelled twice on the x axis for Lactose; the second label should be replaced with ASF356