plot_pmartRseq: Produce a plot of an omicsData Object
In pmartR/pmartRseq: Analysis and Visualization of 16S Data

This function will provide a plot for a omicsData or omicsData_results object.

plot.countSTAT_results(results_object, type = "pvals", test = NULL,
  x_lab = NULL, y_lab = NULL, plot_title = NULL, leglab = NULL,
  FCThresh = log2(1.5), comparison = NULL, ...)

plot.alphaRes(results_object, x_axis = "Group", color = "Group",
  shape = NULL, samplabel = NULL, plot_title = NULL, scales = "free_y",
  x_lab = NULL, y_lab = NULL, leglab = NULL, ...)

plot.evenRes(results_object, x_axis = "Group", color = "Group",
  shape = NULL, samplabel = NULL, plot_title = NULL, scales = "free_y",
  x_lab = NULL, y_lab = NULL, leglab = NULL, ...)

plot.jaccardRes(results_object, variable = "Median", x_axis = "Group",
  color = "Group", shape = NULL, samplabel = NULL, plot_title = NULL,
  x_lab = NULL, y_lab = NULL, leglab = NULL, ...)

plot.countFilter(results_object, breaks = 100, max_count = NULL,
  min_num = NULL, min_samp = NULL, plot_title = NULL, x_lab = NULL,
  y_lab = NULL, ...)

plot.sampleFilter(results_object, breaks = 100, max_count = NULL,
  min_num = NULL, plot_title = NULL, x_lab = NULL, y_lab = NULL, ...)

plot.seqData(results_object, x_axis = "Group", class = "Phylum",
  grp_fn = "median", subset_by = NULL, subset_val = NULL,
  plot_title = NULL, x_lab = NULL, y_lab = NULL, leglab = NULL, ...)

plot.richRes(results_object, abun = NULL, x_axis = "Group",
  color = "Group", scales = "free_y", shape = NULL, samplabel = NULL,
  plot_title = NULL, x_lab = NULL, y_lab = NULL, leglab = NULL, ...)

plot.abunRes(results_object, rich = NULL, x_axis = "Group",
  color = "Group", shape = NULL, samplabel = NULL, plot_title = NULL,
  x_lab = NULL, y_lab = NULL, leglab = NULL, ...)

plot.effspRes(results_object, x_axis = "Group", color = "Group",
  shape = NULL, samplabel = NULL, plot_title = NULL, x_lab = NULL,
  y_lab = NULL, leglab = NULL, ...)

plot.indspRes(results_object, type = "pvals", ...)

plot.paRes(results_object, type = "pvals", ...)

plot.modEnv(results_object, ...)

`results_object`	is an object of class countSTAT_results (`countSTAT`), alphaRes (`alphaDiv_calc`), evenRes (`even_calc`), jaccardRes (`jaccard_calc`), countFilter (`count_based_filter`), sampleFilter (`sample_based_filter`), seqData (`as.seqData`), richRes (`richness_calc`), abunRes (`abundance_calc`), effspRes (`effsp_calc`), indspRes (`indsp_calc`), paRes (`pmartRseq_aldex2`), or modEnv (`mod_env`)
`type`	Character vector specifying which type of plot to create. "pvals" for a line plot showing the number of significantly expresed biomolecules at different p-value thresholds, "flag" for a bar plot showing the number of significantly expressed biomolecules at the previously specified threshold, "logfc" for a heatmap showing the log2 fold changes of the significantly expressed biomolecules, and/or "volcano" for a volcano plot showing the log2 fold changes versus -log10(pvalue). The default is "pvals".
`test`	Optional, a character vector specifying which differential expression test to plot. The default is NULL, which will create plots for all tests.
`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
`plot_title`	Optional, a character vector to use as the plot title
`leglab`	Optional, a character vector to use as the legend label
`FCThresh`	Optional, numeric threshold for the Log2FoldChanges for the volcano plot. Default is log2(1.5)
`x_axis`	Required, a character vector specifying which variable to put on the x-axis, must be one of the column names in attr(results_object, "group_DF"). Default is "Group".
`color`	Optional, a character vector specifying which variable to map to colors, must be one of the column names in attr(results_object, "group_DF"). Default is "Group".
`shape`	Optional, a character vector specifying which variable to map to shape, must be one of the column names in attr(results_object, "group_DF"). Default is NULL.
`samplabel`	Optional, a character vector specifying which variable to map to label, must be equal to fdata cname. Default is NULL.
`scales`	Optional, a character vector to describe if any of the axes should be free when faceting. Default is "free_y" for a free y-axis.
`variable`	Required, character vector specifying Which Jaccard variable to plot - options are "Median", "InterQuartileRange", "Average", and "StdDev". Default is "Median".
`breaks`	Required, a number specifying the number of breaks to have in the cumulative graph. Default is 100.
`max_count`	Optional, a number specifying the maximum count number to show on the graph. Default is NULL.
`min_num`	Optional, a number specifying the desired cut point in order to visualize how many OTUs would be lost if that cut point was used. sum_based_filter uses strictly less than the desired min_num, so this will show the values for strictly less than the desired min_num. Default is NULL. If fn="percent", give the decimal number, not the percentage.
`min_samp`	Optional, for k/a filtering, a number specifying that OTUs must be seen in at least this many samples. Default is 2 for ka filters and NULL for everything else.
`class`	Required, a character vector specifying which variable to group data by (e.g. "Phylum") and to color data by, must be one of the column names in results_object$e_data, results_object$e_meta, or attr(results_object, "group_DF"). Default is "Phylum".
`grp_fn`	Required, a character vector specifying which function to use to summarise values across replicates. Can use one of "median", "mean", or "sum". Default is "median".
`subset_by`	Optional, which variable to subset the data by. NULL will not subset the data. Default is NULL.
`subset_val`	Optional, which values to include in the subset.
`abun`	Optional, an object of class 'abunRes', used for plotting richness vs abundance
`rich`	Optional, an object of class 'richRes', used for plotting richness vs abundance
`plot_title`	Optional, a character vector to use as the plot title
`leglab`	Optional, a character vector to use as the legend label
`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
`x_axis`	Required, a character vector specifying which variable to put on the x-axis, must be one of the column names in attr(results_object, "group_DF"). Default is "Group".
`color`	Optional, a character vector specifying which variable to map to colors, must be one of the column names in attr(results_object, "group_DF"). Default is "Group".
`shape`	Optional, a character vector specifying which variable to map to shape, must be one of the column names in attr(results_object, "group_DF"). Default is NULL.
`samplabel`	Optional, a character vector specifying which variable to map to label, must be equal to fdata cname. Default is NULL.
`scales`	Optional, a character vector to describe if any of the axes should be free when faceting. Default is "free_y" for a free y-axis.
`plot_title`	Optional, a character vector to use as the plot title
`leglab`	Optional, a character vector to use as the legend label
`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
`x_axis`	Required, a character vector specifying which variable to put on the x-axis, must be one of the column names in attr(results_object, "group_DF"). Default is "Group".
`color`	Optional, a character vector specifying which variable to map to colors, must be one of the column names in attr(results_object, "group_DF"). Default is "Group".
`shape`	Optional, a character vector specifying which variable to map to shape, must be one of the column names in attr(results_object, "group_DF"). Default is NULL.
`samplabel`	Optional, a character vector specifying which variable to map to label, must be equal to fdata cname. Default is NULL.
`plot_title`	Optional, a character vector to use as the plot title
`leglab`	Optional, a character vector to use as the legend label
`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
`plot_title`	Optional, a character vector to use as the plot title
`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
`breaks`	Required, a number specifying the number of breaks to have in the cumulative graph. Default is 100.
`max_count`	Optional, a number specifying the maximum count number to show on the graph. Default is NULL.
`min_num`	Optional, a number specifying the desired cut point in order to visualize how many Sampless would be lost if that cut point was used. sample_based_filter uses strictly less than the desired min_num, so this will show the valus for strictly less than the desired min_num. Default is NULL.
`plot_title`	Optional, a character vector to use as the plot title
`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
`x_axis`	Required, a character vector specifying which variable to group data by and put on the x-axis, must be one of the column names in results_object$e_data, results_object$e_meta, or attr(results_object, "group_DF"). Default is "Group".
`plot_title`	Optional, a character vector to use as the plot title
`leglab`	Optional, a character vector to use as the legend label
`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
`x_axis`	Required, a character vector specifying which variable to put on the x-axis, must be one of the column names in attr(results_object, "group_DF"). Default is "Group".
`color`	Optional, a character vector specifying which variable to map to colors, must be one of the column names in attr(results_object, "group_DF"). Default is "Group".
`scales`	Optional, a character vector specifying if any/both of the axes be free. Default is "free_y", for a free y-axis.
`shape`	Optional, a character vector specifying which variable to map to shape, must be one of the column names in attr(results_object, "group_DF"). Default is NULL.
`samplabel`	Optional, a character vector specifying which variable to map to label, must be equal to fdata cname. Default is NULL.
`plot_title`	Optional, a character vector to use as the plot title
`leglab`	Optional, a character vector to use as the legend label
`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
`x_axis`	Required, a character vector specifying which variable to put on the x-axis, must be one of the column names in attr(results_object, "group_DF"). Default is "Group".
`color`	Optional, a character vector specifying which variable to map to colors, must be one of the column names in attr(results_object, "group_DF"). Default is "Group".
`shape`	Optional, a character vector specifying which variable to map to shape, must be one of the column names in attr(results_object, "group_DF"). Default is NULL.
`samplabel`	Optional, a character vector specifying which variable to map to label, must be equal to fdata cname. Default is NULL.
`plot_title`	Optional, a character vector to use as the plot title
`leglab`	Optional, a character vector to use as the legend label
`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
`x_axis`	Required, a character vector specifying which variable to put on the x-axis, must be one of the column names in attr(results_object, "group_DF"). Default is "Group".
`color`	Optional, a character vector specifying which variable to map to colors, must be one of the column names in attr(results_object, "group_DF"). Default is "Group".
`shape`	Optional, a character vector specifying which variable to map to shape, must be one of the column names in attr(results_object, "group_DF"). Default is NULL.
`samplabel`	Optional, a character vector specifying which variable to map to label, must be equal to fdata cname. Default is NULL.
`plot_title`	Optional, a character vector to use as the plot title
`leglab`	Optional, a character vector to use as the legend label
`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
`type`	Required, a character vector specifying which type of plot to create. "pvals" for a line plot showing the number of significantly expresed biomolecules at different p-value thresholds; or "flag" for a bar plot showing the number of indicated species in each group, at the previously specified threshold. The default is "pvals".
`plot_title`	Optional, a character vector to use as the plot title
`leglab`	Optional, a character vector to use as the legend label
`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
`type`	Required, a character vector specifying which type of plot to create. "pvals" for a line plot showing the number of significantly expresed biomolecules at different p-value thresholds; or "flag" for a bar plot showing the number of significantly expressed biomolecules for each term, at the previously specified threshold. The default is "pvals".
`plot_title`	Optional, a character vector to use as the plot title
`leglab`	Optional, a character vector to use as the legend label
`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
`resultsObject`	an object of class 'modEnv', created by `mod_env`
`pval.thresh`	A numeric value used to brighten colour shading where p-values are less than or equal to pval.thresh. Default is 0.05.
`max.size`	The maximum size of the bubble. Default is 20.
`plot_title`	Optional, a character vector to use as the plot title
`leglab`	Optional, a character vector to use as the legend label
`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