Exercise updates #504
Exercise updates #504
Conversation
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really helpful, thanks! |
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I changed the interpretation, removed agglomeration and ajusted the p-values issue. Please let me know if there's anything else i should change. |
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Can you resolve the comments that have been addressed? It will make it easier to track progress. |
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Hi! Thanks for improving the exercises! I added another suggestion in the related issue: #359 (comment) |
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I adjusted the existing heatmap exercise and created a new one using the complexHeatmap package. For the first heatmap, I subsetted the heatmap to use the top taxa and samples by their relative abundance so the heatmap remains readable. |
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I updated the heatmap to use sechm and simplified the subsetting. I'll take a look at the batch transformations now. |
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is there a gap in documentation? |
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The documentation seems to use some deprecated functions in some chapters making it difficult to know which parameters are available for a certain function. Also when querying R using ??function_name it shows the deprecated function rather than the new. |
You are referring to OMA? It should not use deprecated functions, and should be updated. Can you list those problematic chapters and create an issue so that we can fix those? |
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opened it in #519. |
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Hi - can we fix & close this PR? |
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Should be fixed now |
inst/pages/98_exercises.qmd
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Also there is no reply for this (or modification as suggested)
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Some final suggestions. |
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@Insaynoah can you resolve all open points and then confirm if it is ready to merge |
inst/pages/98_exercises.qmd
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| 4. plot a heatmap using the correlations and mark significant correlations (p<0.05)with a cross. |
Sync # Conflicts: # inst/pages/98_exercises.qmd
Co-authored-by: Leo Lahti <[email protected]> Co-authored-by: TuomasBorman <[email protected]>
@AxelDgn and I updated the exercise page as suggested in #359.
The following has been updated