From dfe8f7a119f37a9bd5bce50e32267eea483bd95e Mon Sep 17 00:00:00 2001
From: Caffery Yang <cafferychen7850@gmail.com>
Date: Tue, 9 Jan 2024 17:21:59 +0800
Subject: [PATCH] Delete generate_taxa_association_volcano_long.Rd

---
 man/generate_taxa_association_volcano_long.Rd | 69 -------------------
 1 file changed, 69 deletions(-)
 delete mode 100644 man/generate_taxa_association_volcano_long.Rd

diff --git a/man/generate_taxa_association_volcano_long.Rd b/man/generate_taxa_association_volcano_long.Rd
deleted file mode 100644
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--- a/man/generate_taxa_association_volcano_long.Rd
+++ /dev/null
@@ -1,69 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generate_taxa_association_volcano_long.R
-\name{generate_taxa_association_volcano_long}
-\alias{generate_taxa_association_volcano_long}
-\title{Generate Volcano Plots for Taxa Association Test}
-\usage{
-generate_taxa_association_volcano_long(
-  data.obj,
-  group.var = NULL,
-  test.list,
-  feature.sig.level = 0.1,
-  feature.mt.method = "fdr",
-  palette = c("#F9F871", "#F4A261", "#FF6347"),
-  pdf = FALSE,
-  pdf.wid = 7,
-  pdf.hei = 5
-)
-}
-\arguments{
-\item{data.obj}{A list object in a format specific to MicrobiomeStat, which can include components
-such as feature.tab (matrix), feature.ann (matrix), meta.dat (data.frame), tree,
-and feature.agg.list (list). The data.obj can be converted from other formats using
-several functions from the MicrobiomeStat package, including: 'mStat_convert_DGEList_to_data_obj',
-'mStat_convert_DESeqDataSet_to_data_obj', 'mStat_convert_phyloseq_to_data_obj',
-'mStat_convert_SummarizedExperiment_to_data_obj', 'mStat_import_qiime2_as_data_obj',
-'mStat_import_mothur_as_data_obj', 'mStat_import_dada2_as_data_obj', and
-'mStat_import_biom_as_data_obj'. Alternatively, users can construct their own data.obj.
-Note that not all components of data.obj may be required for all functions in the MicrobiomeStat package.}
-
-\item{group.var}{The grouping variable tested, found in metadata.}
-
-\item{test.list}{The list of test results returned by generate_taxa_trend_test_long.}
-
-\item{feature.sig.level}{The significance level cutoff for highlighting taxa.}
-
-\item{feature.mt.method}{Multiple testing correction method, "fdr" or "none".}
-
-\item{palette}{An optional parameter specifying the color palette to be used for the plot.
-It can be either a character string specifying the name of a predefined
-palette or a vector of color codes in a format accepted by ggplot2
-(e.g., hexadecimal color codes). Available predefined palettes include
-'npg', 'aaas', 'nejm', 'lancet', 'jama', 'jco', and 'ucscgb', inspired
-by various scientific publications and the `ggsci` package. If `palette`
-is not provided or an unrecognized palette name is given, a default color
-palette will be used. Ensure the number of colors in the palette is at
-least as large as the number of groups being plotted.}
-
-\item{pdf}{(optional) Boolean, whether to save the plot as a PDF file.}
-
-\item{pdf.wid}{(optional) Numeric, width of the saved PDF file.}
-
-\item{pdf.hei}{(optional) Numeric, height of the saved PDF file.}
-}
-\value{
-A list of ggplot objects of volcano plots for each taxonomic level.
-}
-\description{
-Generate Volcano Plots for Taxa Association Test
-}
-\examples{
-# Generate test results
-# test_list <- generate_taxa_association_test_long(...)
-# Create volcano plots
-# volcano_plots <- generate_taxa_association_volcano_long(
-#   data.obj, group.var, test_list,
-#   feature.sig.level = 0.05, feature.mt.method = "fdr"
-# )
-
-}