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Install Python and miniconda for MOFA+ #585

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merged 5 commits into from
Jul 29, 2024
Merged

Install Python and miniconda for MOFA+ #585

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c306739
#517 Change: rename cross-correlation to cross-association
artur-sannikov Jul 24, 2024
8b2565a
Merge branch 'rename-cross-correlation' into devel
artur-sannikov Jul 24, 2024
be9a9c0
Change: IntegratedLearner: select pathways and species by FeatureType
artur-sannikov Jul 24, 2024
7e8f446
Fix: install miniconda and Python for MOFA
artur-sannikov Jul 26, 2024
92a99d0
Merge branch 'devel' into install-python-mofa
antagomir Jul 29, 2024
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6 changes: 2 additions & 4 deletions inst/pages/integrated_learner.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -352,7 +352,6 @@ model_concat <- SL_fit_concat$fitLibrary[[1]]$object
# Append the corresponding y and X to the results
SL_fit_concat$Y <- sample_metadata['Y']
SL_fit_concat$X <- fulldat

```

Finally, we consider the intermediate fusion approach, which combines ideas
Expand Down Expand Up @@ -499,7 +498,6 @@ Finally, we visualize the results for the top 20 features for each layer based
on the intermediate fusion.

```{r visualization3, fig.width = 6, fig.height = 7}
#### Change the pathway
# Only plot 20 features per layer
DD <- DD %>%
group_by(view) %>%
Expand Down Expand Up @@ -531,8 +529,8 @@ p <- DD %>%
p
```

Based on the bar plot, we observe that \emph{Proteobacteria_bacterium_CAG.139}
Based on the barplot, we observe that \emph{Proteobacteria_bacterium_CAG.139}
is the species most positively associated, while \emph{Gemmiger_formicilis} is
the most negatively associated species. Additionally, L-lysine biosynthesis VI
is the pathway most positively associated, and PYRIDNUSCYN-PWY: NAD biosynthesis
I (from aspartate) is the pathway most positively associated, respectively.
I (from aspartate) is the pathway most positively associated, respectively.
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