plot_all_diffabun: Plot all differential abundance results
In pmartR/pmartRseq: Analysis and Visualization of 16S Data

Description Usage Arguments Value Author(s) Examples

This function takes the differential abundance results of an omicsData object and creates a plot showing all the log2 fold changes of all features and the corresponding p-values. This looks at the entire dataset to help determine shifts in the whole community.

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plot_all_diffabun(countSTAT_results, omicsData, x_axis = "Phylum",
  scales = "fixed", x_lab = NULL, y_lab = NULL, leglab = NULL,
  plot_title = NULL)

`countSTAT_results`	Required, an object of the class `countSTAT` created by `countSTAT`.
`omicsData`	Required, omicsData ,an object of the class 'seqData' created by `as.seqData`.
`x_axis`	Required, a character vector stating which variable to group data by and put on the x-axis, must be one of "Comparison" or one of the column names in omicsData$e_meta. Default is "Phylum".
`x_lab`	Optional, a character vector to use as the x-axis label
`y_lab`	Optional, a character vector to use as the y-axis label
`leglab`	Optional, a character vector to use as the legend label
`plot_title`	Optional, a character vector to use as the plot title

A plot showing log2 fold change and p-values for all comparisons and all features

Allison Thompson

## Not run: 
library(mintJansson)
library(mintR)
data("rRNAdata")


rRNAdata <- group_designation(omicsData=rRNA_data, main_effects="Treatment")
norm_factors <- normalize_data(omicsData=rRNAdata, subset_fn="none", norm_fn="percentile", normalize=FALSE)
norm_data <- normalize_data(omicsData=rRNAdata, subset_fn="none", norm_fn="percentile", normalize=TRUE)
diffexp <- countSTAT(omicsData=rRNAdata, norm_factors=norm_factors, comparisons="all", test="dw", pval_adjust="none", pval_thresh=0.05)

plot_all_diffabun(countSTAT_results=diffexp, omicsData=norm_data, x_axis="Phylum")

## End(Not run)