maaslin2 --> maaslin3 #656
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Signed-off-by: Daena Rys <[email protected]>
| J. McIver}, | ||
| year = {2020}, | ||
| @Manual{Mallick2024, | ||
| title = {MaAsLin 2: Refining and extending generalized |
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| ```{r run-maaslin2, warning=FALSE, results="hide"} | ||
| ```{r run-maaslin3, warning=FALSE, results="hide"} |
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When you modify these chunk options, please make them to use quarto syntax. --> that way we gradually adopt the full quarto syntax in the book
| Jiaxian and Maharjan, Sagun and Mallick, | ||
| Himel and Franzosa, Eric A. and Thompson, | ||
| Kelsey N. and Nearing, Jacob T. and Huttenhower, Curtis}, | ||
| year = {2024}, | ||
| note = {R/Bioconductor package}, |
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It is not Bioconductor package
| @@ -1136,14 +1136,17 @@ @Article{Das2020 | |||
| microbiomes with bias .pdf} | |||
| } | |||
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| @Manual{Mallick2020, | |||
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Moreover, cite this paper instead
| formula = '~ patient_status', | ||
| normalization = 'TSS', | ||
| transform = 'LOG', | ||
| augment = TRUE, | ||
| standardize = TRUE, | ||
| max_significance = 0.1, | ||
| median_comparison_abundance = TRUE, | ||
| median_comparison_prevalence = FALSE, | ||
| max_pngs = 10, | ||
| cores = 1, |
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Use either " or ', not both. I think " is more common in the book so use it
| head(signif_results, 20) %>% | ||
| dplyr::mutate_if(is.numeric, .funs = function(x){( | ||
| as.character(signif(x, 3)))}) %>% | ||
| knitr::kable() %>% | ||
| kableExtra::kable_styling("striped", position = 'center') %>% | ||
| kableExtra::scroll_box(width = "800px", height = "400px") |
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I think this is too complex and ordinary reader might not understand what is happening here. I think you could just print the table with kable
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Moreover, elsewhere we use functions without defining the package, i.e., knitr::kable() --> kable()
| reference = "patient_status,Control", | ||
| normalization = "TSS", | ||
| standardize = FALSE, | ||
| # filtering was previously performed | ||
| min_prevalence = 0) | ||
| maaslin3_out <- maaslin3(input_data = tse, | ||
| output = "DAA_example", | ||
| formula = '~ patient_status', | ||
| normalization = 'TSS', | ||
| transform = 'LOG', | ||
| augment = TRUE, | ||
| standardize = TRUE, | ||
| max_significance = 0.1, | ||
| median_comparison_abundance = TRUE, | ||
| median_comparison_prevalence = FALSE, | ||
| max_pngs = 10, | ||
| cores = 1, |
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maaslin3 seems to have lots of different options. However, here we just want minimum example.
That would be probably:
maaslin3_out <- maaslin3(
input_data = tse,
output = "DAA_example",
formula = "~ patient_status",
normalization = "TSS",
transform = "LOG",
verbosity = "WARN"
)
| ```{r, summary-plot} | ||
| knitr::include_graphics("DAA_example/figures/summary_plot.png") |
| @@ -34,7 +34,7 @@ gsEasy | |||
| igraph | |||
| IntegratedLearner | |||
| knitr | |||
| Maaslin2 | |||
| maaslin3 | |||
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This should be also added to DESCRIPTION to remotes
| signif_results <- read.csv('DAA_example/significant_results.tsv', | ||
| sep='\t') |
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This does not look good. The indentation is not good
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Is this file the only format for results? I tried to quickly check, but it seems that the summary table is only available in the file
ping #653