.Rbuildignore

@@ -1,2 +1,4 @@
+^renv$
+^renv\.lock$
 ^.*\.Rproj$
 ^\.Rproj\.user$

.Rprofile

@@ -0,0 +1 @@
+source("renv/activate.R")

CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: LMSstat
 Title: AUTOMATION OF STATISTICAL TESTS WITH AN IDENTICAL DATA INPUT.
-Version: 1.0.6
+Version: 1.0.10
 Authors@R: 
     person(given = "CHANG-HO",
            family = "KIM",
@@ -33,7 +33,11 @@ Imports:
     ROCnReg,
     ggrepel,
     circlize,
-    ComplexHeatmap
+    ComplexHeatmap,
+    ape,
+    VennDiagram,
+    rcompanion,
+    data.table
 Depends:
     plyr,
     dplyr

NAMESPACE

@@ -4,12 +4,17 @@ export(AS_barplot)
 export(AS_boxplot)
 export(AS_dotplot)
 export(AS_heatmap)
+export(AS_violinplot)
 export(Allstats)
 export(D_tran)
 export(Indiv_Perm)
 export(Multi_Perm)
 export(NMDS)
+export(Norm_test)
 export(PCA)
+export(PCoA)
+export(SRH)
+export(Volcano)
 export(aroc_compute)
 export(data_summary)
 export(roc_all)

R/AS_barplot.R

@@ -12,6 +12,11 @@
 #' @param width bar width
 #' @param fig_width figure size
 #' @param fig_height figure size
+#' @param Y_text Y axis title size
+#' @param X_text X axis text size
+#' @param Y_lab y axis text size
+#' @param T_size Title size
+#' @param sig_int significance parameter
 #'
 #' @return ggbarplot
 #' @export
@@ -31,7 +36,12 @@ AS_barplot<-function(data,
                      step_increase = 0.05,
                      width = 0.3,
                      fig_width = NA,
-                     fig_height = NA){
+                     fig_height = NA,
+                     X_text = 10,
+                     Y_text = 12,
+                     Y_lab = 10,
+                     T_size =15,
+                     sig_int = c(0.05,0.01)){
   {#Summary
     ###Plot_data_prep###
     ifelse(!dir.exists(file.path(getwd(), "barplot")), dir.create(file.path(getwd(), "barplot")), FALSE)
@@ -54,7 +64,22 @@ AS_barplot<-function(data,
     else if (asterisk =="Dunn"){
       p_val_data<-data[["Dunn"]]}
     else {
-      print("Wrong asterisk input must be one of (Dunn,Scheffe,u_test,t_test)")}}
+      print("Wrong asterisk input must be one of (Dunn,Scheffe,u_test,t_test)")}
+    if(length(unique(data[["Data"]]$Group)) !=2){
+      for(a in 1:nrow(p_val_data)){
+        for(b in 1:ncol(p_val_data)){
+          if(is.nan(p_val_data[a,b])==T){
+            p_val_data[a,b]<-1
+          }
+        }
+      }}
+    else if (length(unique(data[["Data"]]$Group))==2){
+      for(b in 1:length(p_val_data)){
+        if(is.nan(p_val_data[b])==T){
+          p_val_data[b]<-1
+        }
+      }
+    }}
   ###Plots###
   suppressWarnings(
     if (length(unique(data[["Data_renamed"]][["ZZZZ"]]))!=2){
@@ -84,26 +109,25 @@ AS_barplot<-function(data,
       colnames(stat.test) <- c("group1", "group2",
                                "p")
       stat.test<-stat.test %>% plyr::mutate(
-        p.adj.signif = case_when(
-          p > 0.05                   ~ 'NS',
-          p <= 0.05  &p > 0.01                  ~ '*',
-          p <= 0.01                   ~ '**'
+        p.adj.signif = case_when(p >
+                                   sig_int[1] ~ "NS", p <= sig_int[1] & p > sig_int[2] ~ "*",
+                                 p <= sig_int[2] ~ "**"
         )
       )
       stat.test<-stat.test[stat.test$p.adj.signif != "NS",]
       if (length(stat.test>4)){
         ggpubr::ggbarplot(df,
                           x = "Group",
                           y ="len",
-                          color = ckey,
+                          color = NA,
                           fill ="Group",
                           palette = ckey,
                           order = order,
                           width = width) +
           ggplot2::geom_errorbar( ggplot2::aes(x=Group, ymin=len-SEM, ymax=len+SEM), width=0.2, colour="Black", alpha=1, size=0.5)+
           ggplot2::scale_y_continuous(label=ecoflux::scientific_10x)+
           ggplot2::labs(title=NAMES[number],x =NULL, y = "Intensity")+
-          ggplot2::theme_classic()+ ggplot2::theme(plot.title=ggplot2::element_text(size=15,
+          ggplot2::theme_classic()+ ggplot2::theme(plot.title=ggplot2::element_text(size=T_size,
                                                          face="bold",
                                                          color="Black",
                                                          hjust=0.5,
@@ -113,10 +137,10 @@ AS_barplot<-function(data,
                                  plot.caption=ggplot2::element_text(size=15),  # caption
                                  axis.title.x=ggplot2::element_text(vjust=10,
                                                            size=15),  # X axis title
-                                 axis.title.y=ggplot2::element_text(size=12),  # Y axis title
-                                 axis.text.x=ggplot2::element_text(size=10,
+                                 axis.title.y=ggplot2::element_text(size=Y_text),  # Y axis title
+                                 axis.text.x=ggplot2::element_text(size=X_text,
                                                           vjust=.5),  # X axis text
-                                 axis.text.y=ggplot2::element_text(size=10),
+                                 axis.text.y=ggplot2::element_text(size=Y_lab),
                                  legend.position = legend_position)+
           ggpubr::stat_pvalue_manual(stat.test,
                                      y.position = 1.05 * max(data[["Data_renamed"]][,number]),
@@ -133,15 +157,15 @@ AS_barplot<-function(data,
       else if(significant_variable_only == F) {
         ggpubr::ggbarplot(df,x = "Group",
                           y ="len",
-                          color = ckey,
+                          color = NA,
                           fill ="Group",
                           palette = ckey,
                           order = order,
                           width = width) +
           ggplot2::geom_errorbar( ggplot2::aes(x=Group, ymin=len-SEM, ymax=len+SEM), width=0.2, colour="Black", alpha=1, size=0.5)+
           ggplot2::scale_y_continuous(label=ecoflux::scientific_10x)+
           ggplot2::labs(title=NAMES[number],x =NULL, y = "Intensity")+
-          ggplot2::theme_classic()+ ggplot2::theme(plot.title=ggplot2::element_text(size=15,
+          ggplot2::theme_classic()+ ggplot2::theme(plot.title=ggplot2::element_text(size=T_size,
                                                                            face="bold",
                                                                            color="Black",
                                                                            hjust=0.5,
@@ -151,10 +175,10 @@ AS_barplot<-function(data,
                                                    plot.caption=ggplot2::element_text(size=15),  # caption
                                                    axis.title.x=ggplot2::element_text(vjust=10,
                                                                              size=15),  # X axis title
-                                                   axis.title.y=ggplot2::element_text(size=12),  # Y axis title
-                                                   axis.text.x=ggplot2::element_text(size=10,
+                                                   axis.title.y=ggplot2::element_text(size=Y_text),  # Y axis title
+                                                   axis.text.x=ggplot2::element_text(size=X_text,
                                                                             vjust=.5),  # X axis text
-                                                   axis.text.y=ggplot2::element_text(size=10),
+                                                   axis.text.y=ggplot2::element_text(size=Y_lab),
                                  legend.position = legend_position)
 
         ggplot2::ggsave(filename = paste(NAMES[number],"barplot.jpg",collapse = ""),
@@ -206,23 +230,23 @@ AS_barplot<-function(data,
         colnames(stat.test) <- c("group1", "group2",
                                  "p")
         stat.test <- stat.test %>% plyr::mutate(p.adj.signif = case_when(p >
-                                                                           0.05 ~ "NS", p <= 0.05 & p > 0.01 ~ "*",
-                                                                         p <= 0.01 ~ "**"))
+                                                                           sig_int[1] ~ "NS", p <= sig_int[1] & p > sig_int[2] ~ "*",
+                                                                         p <= sig_int[2] ~ "**"))
         stat.test <- stat.test[stat.test$p.adj.signif !=
                                  "NS", ]
         if (length(stat.test>4)){
           ggpubr::ggbarplot(df,
                             x = "Group",
                             y ="len",
-                            color = ckey,
+                            color = NA,
                             fill ="Group",
                             palette = ckey,
                             order = order,
                             width = width) +
             ggplot2::geom_errorbar( ggplot2::aes(x=Group, ymin=len-SEM, ymax=len+SEM), width=0.2, colour="Black", alpha=1, size=0.5)+
             ggplot2::scale_y_continuous(label=ecoflux::scientific_10x)+
             ggplot2::labs(title=NAMES[number],x =NULL, y = "Intensity")+
-            ggplot2::theme_classic()+ ggplot2::theme(plot.title=ggplot2::element_text(size=15,
+            ggplot2::theme_classic()+ ggplot2::theme(plot.title=ggplot2::element_text(size=T_size,
                                                                     face="bold",
                                                                     color="Black",
                                                                     hjust=0.5,
@@ -232,10 +256,10 @@ AS_barplot<-function(data,
                                             plot.caption=ggplot2::element_text(size=15),  # caption
                                             axis.title.x=ggplot2::element_text(vjust=10,
                                                                       size=15),  # X axis title
-                                            axis.title.y=ggplot2::element_text(size=12),  # Y axis title
-                                            axis.text.x=ggplot2::element_text(size=10,
+                                            axis.title.y=ggplot2::element_text(size=Y_text),  # Y axis title
+                                            axis.text.x=ggplot2::element_text(size=X_text,
                                                                      vjust=.5),  # X axis text
-                                            axis.text.y=ggplot2::element_text(size=10),
+                                            axis.text.y=ggplot2::element_text(size=Y_lab),
                                             legend.position = legend_position)+
             ggpubr::stat_pvalue_manual(stat.test,
                                        y.position = 1.05 * max(data[["Data_renamed"]][,number]),
@@ -253,15 +277,15 @@ AS_barplot<-function(data,
           ggpubr::ggbarplot(df,
                             x = "Group",
                             y ="len",
-                            color = ckey,
+                            color = NA,
                             fill ="Group",
                             palette = ckey,
                             order = order,
                             width = width) +
             ggplot2::geom_errorbar( ggplot2::aes(x=Group, ymin=len-SEM, ymax=len+SEM), width=0.2, colour="Black", alpha=1, size=0.5)+
             ggplot2::scale_y_continuous(label=ecoflux::scientific_10x)+
             ggplot2::labs(title=NAMES[number],x =NULL, y = "Intensity")+
-            ggplot2::theme_classic()+ ggplot2::theme(plot.title=ggplot2::element_text(size=15,
+            ggplot2::theme_classic()+ ggplot2::theme(plot.title=ggplot2::element_text(size=T_size,
                                                            face="bold",
                                                            color="Black",
                                                            hjust=0.5,
@@ -271,10 +295,10 @@ AS_barplot<-function(data,
                                    plot.caption=ggplot2::element_text(size=15),  # caption
                                    axis.title.x=ggplot2::element_text(vjust=10,
                                                              size=15),  # X axis title
-                                   axis.title.y=ggplot2::element_text(size=12),  # Y axis title
-                                   axis.text.x=ggplot2::element_text(size=10,
+                                   axis.title.y=ggplot2::element_text(size=Y_text),  # Y axis title
+                                   axis.text.x=ggplot2::element_text(size=X_text,
                                                             vjust=.5),  # X axis text
-                                   axis.text.y=ggplot2::element_text(size=10),
+                                   axis.text.y=ggplot2::element_text(size=Y_lab),
                                    legend.position = legend_position)
 
           ggplot2::ggsave(filename = paste(NAMES[number],"barplot.jpg",collapse = ""),