Rarecurve output range
Nobody has claimed this yet.
Assessment
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Newbie friendliness
- 25/100
- Issue type
- Feature
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- r
- Domain
- data-visualization
Research direction
Start with the calls to mp_rrarefy(), mp_cal_rarecurve(), and mp_plot_rarecurve(), then inspect the generated RareAbundanceRarecurve data and the plot coordinate limits. Determine whether the depth is limited during rarecurve calculation or only during plotting; done means the output can represent depth up to 2e7 reads and the requested observations range.
Written by the indexing model from the issue text.
Description
Hello...I apologize if this question seems basic, but I was wondering if you could help me figure out how to increase the range of the outputted rarecurve (i.e. the depth [readsNums] and observations [value]). I wish to see the depth up to 2e7 reads. I tried to simply extend the coordinates of the output but this did not work. Thank you for your time!
Code:
mpse %<>% mp_rrarefy() %<>%
mp_cal_rarecurve(
.abundance = Abundance,
chunks = 350, action = "add", force=FALSE
)
set.seed(1234)
plotmpse<- mpse %>%
mp_plot_rarecurve(
.rare = RareAbundanceRarecurve,
.alpha = "Observe",
.group = CollectionPhase,
plot.group = TRUE
) + theme_bw() + coord_cartesian(xlim=c(0,2000), ylim = c(0,100))+
scale_color_manual(values=c("#789ED0", "#F79D40", "#72BF56", "#E4655A", "#AB8BCB")) +
scale_fill_manual(values=c("#789ED0", "#F79D40", "#72BF56", "#E4655A", "#AB8BCB"))
plotmpse
- Dominant language
- R
- Stars
- 196
- Forks
- 36
- PR merge metrics
- No merged PRs in 30d
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