rename function with module nam

lixiang117423 · Jan 3, 2025 · d3fa858 · d3fa858
1 parent 6d88f57
commit d3fa858
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Showing 17 changed files with 92 additions and 90 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,19 +1,19 @@
 # Generated by roxygen2: do not edit by hand
 
-export(PCA)
-export(PCoA)
-export(call_DAMs_DESeq2)
-export(call_DAMs_LEfSe)
-export(call_DEGs_DESeq2)
-export(cor_and_plot)
-export(enrich_GO)
-export(enrich_KEGG)
-export(find_outliner)
-export(lm_and_plot)
-export(plot_theme)
-export(plot_volcano)
-export(reorder2heatmap)
-export(top_10)
+export(CommonlyUsed.PCA)
+export(CommonlyUsed.cor_and_plot)
+export(CommonlyUsed.find_outliner)
+export(CommonlyUsed.lm_and_plot)
+export(CommonlyUsed.plot_theme)
+export(CommonlyUsed.reorder2heatmap)
+export(Microbiome.PCoA)
+export(Microbiome.call_DAMs_DESeq2)
+export(Microbiome.call_DAMs_LEfSe)
+export(Microbiome.top_10)
+export(RNASeq.call_DEGs_DESeq2)
+export(RNASeq.enrich_GO)
+export(RNASeq.enrich_KEGG)
+export(RNASeq.plot_volcano)
 importFrom(DESeq2,DESeq)
 importFrom(DESeq2,DESeqDataSetFromMatrix)
 importFrom(DESeq2,results)

diff --git a/R/Microbiome.call_DAMs_DESeq2.R b/R/Microbiome.call_DAMs_DESeq2.R
@@ -6,7 +6,7 @@
 #' @param log2FoldChange The threshold for the absolute value of log2FoldChange is set to 1 by default.
 #' @param padj The threshold for the adjusted p-value is set to 0.05 by default.
 #'
-#' @return
+#' @return A data frame from DESeq2.
 #' @export
 #'
 #' @examples
@@ -32,7 +32,7 @@ Microbiome.call_DAMs_DESeq2 <- function(data, sample, group = "group", log2FoldC
       log2FoldChange < -{{ log2FoldChange }} & padj < {{ padj }} ~ "Depleted",
       TRUE ~ "NS"
     )) %>%
-    tibble::rownames_to_column(var = "OTU") -> dems
+    tibble::rownames_to_column(var = "OTU") -> dams
 
-  return(dems)
+  return(dams)
 }
diff --git a/deve.log.R b/deve.log.R
@@ -129,7 +129,6 @@ dir("R") %>%
 
 123
 
-
 # 编译vignettes
 # usethis::use_vignette(name = "pca_in_one") # 运行第二次会覆盖之前的
 # usethis::use_vignette(name = "cor_and_plot")

diff --git a/man/PCA.Rd → man/CommonlyUsed.PCA.Rd b/man/PCA.Rd → man/CommonlyUsed.PCA.Rd
diff --git a/man/cor_and_plot.Rd → man/CommonlyUsed.cor_and_plot.Rd b/man/cor_and_plot.Rd → man/CommonlyUsed.cor_and_plot.Rd
diff --git a/man/find_outliner.Rd → man/CommonlyUsed.find_outliner.Rd b/man/find_outliner.Rd → man/CommonlyUsed.find_outliner.Rd
diff --git a/man/lm_and_plot.Rd → man/CommonlyUsed.lm_and_plot.Rd b/man/lm_and_plot.Rd → man/CommonlyUsed.lm_and_plot.Rd
diff --git a/man/plot_theme.Rd → man/CommonlyUsed.plot_theme.Rd b/man/plot_theme.Rd → man/CommonlyUsed.plot_theme.Rd
diff --git a/man/reorder2heatmap.Rd → man/CommonlyUsed.reorder2heatmap.Rd b/man/reorder2heatmap.Rd → man/CommonlyUsed.reorder2heatmap.Rd
diff --git a/man/PCoA.Rd → man/Microbiome.PCoA.Rd b/man/PCoA.Rd → man/Microbiome.PCoA.Rd
diff --git a/man/call_DAMs_DESeq2.Rd → man/Microbiome.call_DAMs_DESeq2.Rd b/man/call_DAMs_DESeq2.Rd → man/Microbiome.call_DAMs_DESeq2.Rd
diff --git a/man/call_DAMs_LEfSe.Rd → man/Microbiome.call_DAMs_LEfSe.Rd b/man/call_DAMs_LEfSe.Rd → man/Microbiome.call_DAMs_LEfSe.Rd
diff --git a/man/top_10.Rd → man/Microbiome.top_10.Rd b/man/top_10.Rd → man/Microbiome.top_10.Rd
diff --git a/man/call_DEGs_DESeq2.Rd → man/RNASeq.call_DEGs_DESeq2.Rd b/man/call_DEGs_DESeq2.Rd → man/RNASeq.call_DEGs_DESeq2.Rd
diff --git a/man/enrich_GO.Rd → man/RNASeq.enrich_GO.Rd b/man/enrich_GO.Rd → man/RNASeq.enrich_GO.Rd
diff --git a/man/enrich_KEGG.Rd → man/RNASeq.enrich_KEGG.Rd b/man/enrich_KEGG.Rd → man/RNASeq.enrich_KEGG.Rd
diff --git a/man/plot_volcano.Rd → man/RNASeq.plot_volcano.Rd b/man/plot_volcano.Rd → man/RNASeq.plot_volcano.Rd
Original file line number	Diff line number	Diff line change
Expand Up		@@ -129,7 +129,6 @@ dir("R") %>%

		123


		# 编译vignettes
		# usethis::use_vignette(name = "pca_in_one") # 运行第二次会覆盖之前的
		# usethis::use_vignette(name = "cor_and_plot")
Expand Down