From aee9e1b713c5df4692c62772f1d225e92d9a7087 Mon Sep 17 00:00:00 2001
From: lixiang <lixiang117423@gmail.com>
Date: Thu, 2 Jan 2025 09:59:42 +0800
Subject: [PATCH] update cor_and_plot

---
 NAMESPACE                  | 67 --------------------------------------
 R/cor_and_plot.R           |  4 +--
 vignettes/cor_and_plot.Rmd |  2 +-
 3 files changed, 3 insertions(+), 70 deletions(-)
 delete mode 100644 NAMESPACE

diff --git a/NAMESPACE b/NAMESPACE
deleted file mode 100644
index 7c18c7d..0000000
--- a/NAMESPACE
+++ /dev/null
@@ -1,67 +0,0 @@
-# Generated by roxygen2: do not edit by hand
-
-export(PCA)
-export(PCoA)
-export(call_DEGs_DESeq2)
-export(call_DEMs_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)
-importFrom(DESeq2,DESeq)
-importFrom(DESeq2,DESeqDataSetFromMatrix)
-importFrom(DESeq2,results)
-importFrom(FactoMineR,PCA)
-importFrom(WGCNA,corAndPvalue)
-importFrom(ape,pcoa)
-importFrom(clusterProfiler,enricher)
-importFrom(dplyr,"%>%")
-importFrom(dplyr,arrange)
-importFrom(dplyr,count)
-importFrom(dplyr,inner_join)
-importFrom(dplyr,left_join)
-importFrom(dplyr,mutate)
-importFrom(dplyr,rename)
-importFrom(dplyr,select)
-importFrom(dplyr,slice_max)
-importFrom(factoextra,get_eigenvalue)
-importFrom(ggplot2,aes)
-importFrom(ggplot2,element_blank)
-importFrom(ggplot2,element_line)
-importFrom(ggplot2,element_rect)
-importFrom(ggplot2,element_text)
-importFrom(ggplot2,geom_hline)
-importFrom(ggplot2,geom_point)
-importFrom(ggplot2,geom_smooth)
-importFrom(ggplot2,geom_vline)
-importFrom(ggplot2,ggplot)
-importFrom(ggplot2,guides)
-importFrom(ggplot2,labs)
-importFrom(ggplot2,position_fill)
-importFrom(ggplot2,rel)
-importFrom(ggplot2,theme)
-importFrom(ggplot2,unit)
-importFrom(ggprism,guide_prism_offset_minor)
-importFrom(ggsci,scale_color_d3)
-importFrom(ggthemes,theme_foundation)
-importFrom(magrittr,set_names)
-importFrom(purrr,map)
-importFrom(purrr,map_dbl)
-importFrom(rlang,sym)
-importFrom(rstatix,wilcox_test)
-importFrom(scales,percent)
-importFrom(stats,IQR)
-importFrom(stats,anova)
-importFrom(stats,quantile)
-importFrom(stats,reorder)
-importFrom(stringr,str_replace)
-importFrom(stringr,str_split)
-importFrom(tibble,rownames_to_column)
-importFrom(tidyr,nest)
-importFrom(tidyr,pivot_longer)
-importFrom(vegan,vegdist)
diff --git a/R/cor_and_plot.R b/R/cor_and_plot.R
index 6eb1fa1..656c54d 100644
--- a/R/cor_and_plot.R
+++ b/R/cor_and_plot.R
@@ -35,7 +35,7 @@ cor_and_plot <- function(data.1, data.2 = NULL, method = "pearson", cor = 0.6, p
       tidyr::pivot_longer(cols = 2:ncol(.), names_to = "to", values_to = "pvalue") -> df.pvalue
 
     dplyr::left_join(df.cor, df.pvalue) %>%
-      dplyr::filter(pvalue <= {{ pvalue }}, cor >= {{ cor }}, from != to) -> result.cor
+      dplyr::filter(pvalue <= {{ pvalue }}, abs(cor) >= {{ cor }}, from != to) -> result.cor
   } else {
     WGCNA::corAndPvalue(x = {{ data.1 }}, y = {{ data.2 }}, method = {{ method }}) -> cor.res
 
@@ -50,7 +50,7 @@ cor_and_plot <- function(data.1, data.2 = NULL, method = "pearson", cor = 0.6, p
       tidyr::pivot_longer(cols = 2:ncol(.), names_to = "to", values_to = "pvalue") -> df.pvalue
 
     dplyr::left_join(df.cor, df.pvalue) %>%
-      dplyr::filter(pvalue <= {{ pvalue }}, cor >= {{ cor }}, from != to) -> result.cor
+      dplyr::filter(pvalue <= {{ pvalue }}, abs(cor) >= {{ cor }}, from != to) -> result.cor
   }
 
   # return
diff --git a/vignettes/cor_and_plot.Rmd b/vignettes/cor_and_plot.Rmd
index 5793490..0ac8dff 100644
--- a/vignettes/cor_and_plot.Rmd
+++ b/vignettes/cor_and_plot.Rmd
@@ -14,6 +14,6 @@ knitr::opts_chunk$set(
 )
 ```
 
-```{r, eval = FALSE}
+```{r setup}
 library(biohelpers)
 ```