add: variables topX and normalize to Phyloseq Bar Plot #6665
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tools/phyloseq/phyloseq_plot_bar.R
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| @@ -49,14 +58,52 @@ if (is.null(opt$output) || opt$output == "") { | |||
| print(paste("Trying to read:", opt$input)) | |||
| physeq <- readRDS(opt$input) | |||
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| print(rank_names(physeq)) | |||
tools/phyloseq/phyloseq_plot_bar.xml
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| ]]></command> | ||
| <inputs> | ||
| <expand macro="phyloseq_input"/> | ||
| <param name="x" type="text" label="X-axis variable" help="Variable for the x-axis (e.g., Sample, Phylum)" /> | ||
| <param name="fill" type="text" label="Fill variable" help="Variable to color the bars (e.g., Genus, Order)" /> | ||
| <param name="facet" type="text" optional="true" label="Facet by variable" help="Optional: Variable to facet the chart by (e.g., SampleType)" /> | ||
| <param name="topX" type="integer" optional="true" label="Top X" help="Optional: Only show the top X values" /> | ||
| <param name="keepOthers" type="boolean" optional="true" label="Keep 'Others'" help="Optional: Keep an 'Others' category for values not in the top X" /> |
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Boolean parameters can't be optional.
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@MaraBesemer can you remove the optional and add a value for topX ? 10 should be a good default.
tools/phyloseq/phyloseq_plot_bar.xml
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| ]]></command> | ||
| <inputs> | ||
| <expand macro="phyloseq_input"/> | ||
| <param name="x" type="text" label="X-axis variable" help="Variable for the x-axis (e.g., Sample, Phylum)" /> | ||
| <param name="fill" type="text" label="Fill variable" help="Variable to color the bars (e.g., Genus, Order)" /> | ||
| <param name="facet" type="text" optional="true" label="Facet by variable" help="Optional: Variable to facet the chart by (e.g., SampleType)" /> | ||
| <param name="topX" type="integer" optional="true" label="Top X" help="Optional: Only show the top X values" /> | ||
| <param name="keepOthers" type="boolean" optional="true" label="Keep 'Others'" help="Optional: Keep an 'Others' category for values not in the top X" /> | ||
| <param name="normalize" type="boolean" optional="true" label="Normalize" help="Optional: Normalize abundances to sum to 100%" /> |
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What happens if you normalize and do not keep others?
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the way I wrote the script, normalization happens after pruning. Now that I think about it, the other way around makes more sense. I did to allow renormalization when unassigned OTUs are present. But now I adjusted the script to assign those cases as unassigned. MaraBesemer#2
With this update, the normalization is done first and then pruning. So if you normalize and do not keep others you get something like:
and with others:
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@MaraBesemer can you also add wrapper options for To the wrapper ? Usually one needs to play around a bit with this, device should allow at least for pdf, png and some of: https://ggplot2.tidyverse.org/reference/ggsave.html |
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