Need advice: labels for x-axis in comp_barplot() (calculate dominant taxon walkthrough) #138
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RachBioHaz
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Glad you're finding the package useful :) Something like this code below is maybe helpful? the trick being pasting the dominant taxon variable and the subject or sample variable together into a new variable and then specifying that as the bar label library(ggplot2)
library(microViz)
#> microViz version 0.12.1 - Copyright (C) 2021-2024 David Barnett
#> ! Website: https://david-barnett.github.io/microViz
#> ✔ Useful? For citation details, run: `citation("microViz")`
#> ✖ Silence? `suppressPackageStartupMessages(library(microViz))`
ps <- microViz::ibd %>%
tax_filter(min_prevalence = 3) %>%
tax_fix()
# "portrait" orientation, to fit long labels
ps %>%
ps_filter(DiseaseState == "CD", age < 14) %>%
ps_calc_dominant(rank = "Genus", var = "dominant_genus") %>%
ps_mutate(sample_and_genus = paste(sample, dominant_genus, sep = ": ")) %>%
comp_barplot(tax_level = "Genus", label = "sample_and_genus", n_taxa = 12) +
coord_flip()
#> Registered S3 method overwritten by 'seriation':
#> method from
#> reorder.hclust vegan# or "landscape" with linebreaks, if you have enough space for the labels
ps %>%
ps_filter(DiseaseState == "CD", age < 14, gender == "female") %>%
ps_calc_dominant(rank = "Genus", var = "dominant_genus") %>%
ps_mutate(sample_and_genus = paste(sample, dominant_genus, sep = "\n")) %>%
comp_barplot(tax_level = "Genus", label = "sample_and_genus", n_taxa = 12)Created on 2024-01-27 with reprex v2.1.0 Session infosessioninfo::session_info()
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That's exactly what I was after - thank you. |
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Hi,
loving this package - especially since I am new(ish) to R and ggplot can be hard to navigate. I am hoping someone can give me some advice about the x-axis label.
I am following the walkthrough on dominant taxa barplots (https://david-barnett.github.io/microViz/reference/ps_calc_dominant.html) and I wanted to add a second x-axis label. At the moment I am selecting either to label the x axis with "dominant_Genus" or "subject id".
I would like to be able to display the most abundant taxa on the x-axis but also want to display the subject id, either, next to it, on a secondary x-axis or as an annotation on the stacked bar - however I have had no luck with ggplot.
Can anyone propose any suggestions that do not require me to look too deeply under the bonnet of ggplot to get it to work?
Thanks
Rachele
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