MiHC.plot: The Q-Q plots for the microbiome higher criticism analysis

In hk1785/MiHC: Microbiome Higher Criticism Analysis

The Q-Q plots for the microbiome higher criticism analysis

Description

This function produces Q-Q plots for the microbiome higher criticism analysis.

Usage

MiHC.plot(MiHC.out, leg.loc="bottomright", pdf.filename=NULL)

Arguments

MiHC.out	An output obtained using the MiHC function.
leg.loc	The legend location to list the top 10 influential OTUs. Default is leg.loc="bottomright".
pdf.filename	The PDF filename to print the figure as a PDF file. Default is pdf.filename=NULL to print the figure on the R graphics window.

Value

The Q-Q plots between the expected and observed quantiles for the unweighted and weighted higher criticism tests. Blue dots represent individual OTUs and a red diagonal line represents no influential points; as such, the OTUs that fall along the diagonal line have no influence on the host phenotype while the OTUs that have larger deviations from the diagonal line are more influential on the host phenotype. Darker to lighter vertical lines represent more to less influential OTUs in rank order among the 10 most influential OTUs that correspond to the 10 largest deviations from the red diagonal line.

Author(s)

Hyunwook Koh

References

Koh and Zhao. A powerful microbial group association test based on the higher criticism analysis for sparse microbial association signals. (Under revision).

Simes (1986). An improved Bonferroni procedure for multiple tests of significance. Biometrika.73(3):751-754

Examples

# Import requisite R packages
require(cluster)
require(compositions)
require(permute)
require(phyloseq)

# Import example microbiome data
data(phy)
otu.tab <- otu_table(phy)
tree <- phy_tree(phy)
y <- sample_data(phy)$y
covs <- data.frame(matrix(NA, length(y), 2))
covs[,1] <- as.numeric(sample_data(phy)$x1)
covs[,2] <- as.factor(sample_data(phy)$x2)

# Fit MiHC
set.seed(123)
out <- MiHC(y, covs=covs, otu.tab=otu.tab, tree=tree, model="binomial", n.perm=1000)
out

# Create plots
MiHC.plot(MiHC.out=out)

hk1785/MiHC documentation built on Dec. 21, 2024, 4:29 a.m.