This function calculates for each feature a pseudo-fold change (geometrical mean of the difference between quantiles) between the different classes found in labels.
Significance of the differences is computed for each feature using a Wilcoxon test followed by multiple hypothesis testing correction.
Additionally, the Area Under the Receiver Operating Characteristic Curve
(AU-ROC) and a prevalence shift are computed for the features found to be
associated with the two different classes at a user-specified
significance level alpha
.
Finally, the function produces a plot of the top max.show
associated features, showing the distribution of the log10-transformed
abundances for both classes, and user-selected panels for the effect
(AU-ROC, Prevalence Shift, and Fold Change)
check.associations(siamcat,fn.plot,color.scheme = "RdYlBu", alpha =0.05,mult.corr = "fdr", sort.by = "fc",detect.lim = 1e-06, pr.cutoff = 1e-6, max.show = 50, plot.type = "quantile.box", panels = c("fc","auroc"),verbose = 1)
siamcat | object of class siamcat-class |
---|---|
fn.plot | filename for the pdf-plot |
color.scheme | valid R color scheme or vector of valid R colors (must be
of the same length as the number of classes), defaults to |
alpha | float, significance level, defaults to |
mult.corr | multiple hypothesis correction method, see
|
sort.by | string, sort features by p-value ( |
detect.lim | float, pseudocount to be added before log-transformation of
the data, defaults to |
pr.cutoff | float, cutoff for the prevalence computation, defaults to
|
max.show | integer, how many associated features should be shown,
defaults to |
plot.type | string, specify how the abundance should be plotted, must be
one of these: |
panels | vector, name of the panels to be plotted next to the log10-
transformed abundances, possible entries are |
verbose | control output: |
Does not return anything, but produces an association plot
# Example data data(siamcat_example) # since the whole pipeline has been run in the example data, exchange the # normalized features with the original features siamcat_example <- reset.features(siamcat_example) # Simple example check.associations(siamcat_example, './assoc_plot.pdf')#> Error in label$info: $ operator not defined for this S4 class# Plot associations as bean plot check.associations(siamcat_example, './assoc_plot_bean.pdf', plot.type='bean')#> Error: $ operator not defined for this S4 class# Plot assocations as box plot # Additionally, sort by p-value instead of by fold change check.associations(siamcat_example, './assoc_plot_fc.pdf', plot.type='box', sort.by='p.val')#> Error: $ operator not defined for this S4 class# Custom colors check.associations(siamcat_example, './assoc_plot_blue_yellow.pdf', plot.type='box', color.scheme=c('cornflowerblue', '#ffc125'))#> Error: $ operator not defined for this S4 class