1118 mass balance #1136
1118 mass balance #1136
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| { | ||
| "Name": "Intracellular", | ||
| "Include": [ | ||
| "Organism|**|Intracellular|Aciclovir*" |
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I forgot what we decided: if the molecules list above includes only Aciclovir,
but I have e.g. Aciclovir-XY-Metabolite in my simulation:
will Aciclovir-XY-Metabolite be included via "Organism|**|Intracellular|Aciclovir*" or not?
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Yes, I stated it in the vignette
Note that inclusion and exclusion criteria for molecule paths leverage wild card symbols (*).
...
Another use case is when a metabolite is defined using the molecule name as prefix.
Then, the metabolite can be included in the grouping.
{
"Name": "Plasma for Aciclovir and metabolites",
"Include": ["Organism|**|Plasma|Aciclovir*"]
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What I meant: the molecules list in the example contains Aciclovir only:
"Molecules": [
"Aciclovir"
],
Now if "Include": ["Organism|**|Plasma|Aciclovir*"] retrieves both Aciclovir and Aciclovir-XY-Metabolite: will the metabolite be included or not?
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Since only aciclovir was in molecules, no, they should not be retreived from the search.
(because the interesection between all the molecule paths from the compound in Molecules field and the Include field is used).
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ok. it would be good to select another example for vignette, which incorporates metabolites as well - but let's keep Aciclovir for now AS IS.
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created an issue for that: #1148
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R/utilities-mass-balance.R
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| if(!isEmpty(plotSettings$Name)){ | ||
| sectionId <- defaultFileNames$resultID(length(massBalanceResults) + 1, "mass_balance") | ||
| massBalanceResults[[sectionId]] <- saveTaskResults( | ||
| id = sectionId, | ||
| textChunk = paste("###", plotSettings$Name, anchor(sectionId)), | ||
| includeTextChunk = TRUE | ||
| ) | ||
| } |
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what happens if plotSettings$Name is empty?
Somehow I cannot see the else-part (where the default subchapter caption is written)
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Currently, there is no sub section title added if plotSettings$Name is empty.
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