Description Usage Arguments Author(s) See Also Examples
By specifying the phylogenic level, coeficient, and cutoff, all the taxa with a adjusted or unadjusted p value that is smaller than the cutoff will be selected. Then the summarized OTU table at the specifed level is extracted to generate a heatmap.
This function depends on the zheatmap
package. The package can
be installed from the github using devtools::install_github("zhuchcn/zheatmap")
1 2 | plot_heatmap(spy, spys, level = "Genus", coef = "pvalue",
cutoff = 0.05, anno.var, ...)
|
spy |
SummarizedPhyloseq object |
spys |
SummarizedPhyloStats object |
level |
character variable indicates the targeted phylogenic level |
coef |
character, either "pvalue" or "padj" |
cutoff |
numeric, the cutoff of coef to use |
anno.var |
character, indicates the sample metadata variabel to use for annotation as a side bar. It must be one from the colnames of the sample data. |
... |
other parameters supported by the |
Chenghao Zhu
SummarizedPhyloseq-class
, SummarizedPhyloStats-class
, zheatmap
1 2 3 4 5 6 7 8 9 10 | data(fatigue)
fatigue = transform_sample_counts(fatigue, function(x) x/sum(x))
spy = summarizeFromPhyloseq(fatigue)
design = model.matrix(data = as(sample_data(fatigue), "data.frame"), ~Subject + 1)
spys_lm = spy_to_limma(spy_prop, design, transform = "log", p.value = 2, coef = 2)
plot_heatmap(spy,
spys_lm,
coef = "pvalue",
cutoff = 0.1,
anno.var = "Subject")
|
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