PomaNormPlot

.Rbuildignore

@@ -2,3 +2,4 @@
 ^\.Rproj\.user$
 ^\.travis\.yml$
 ^codecov\.yml$
+^LICENSE\.md$

.travis.yml

@@ -1,10 +1,13 @@
 # R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
 
-language: R
-cache: packages
+language: r
+
+r_packages:
+  - covr
+  - devtools
 
 r_github_packages:
-  - r-lib/covr
+  - codecov/POMA
 
 after_success:
-  - Rscript -e 'covr::codecov()'
+  - Rscript -e 'library(covr);codecov()'

DESCRIPTION

@@ -1,17 +1,24 @@
 Package: POMA
-Title: What the Package Does (One Line, Title Case)
+Title: R Package for Statistical Analysis of Metabolomic Data
 Version: 0.0.0.9000
 Authors@R: 
-    person(given = "First",
-           family = "Last",
+    person(given = "Pol",
+           family = "Castellano-Escuder",
            role = c("aut", "cre"),
-           email = "first.last@example.com",
-           comment = c(ORCID = "YOUR-ORCID-ID"))
+           email = "polcaes@gmail.com",
+           comment = c(ORCID = "0000-0001-6466-877X"))
 Description: What the package does (one paragraph).
-License: What license it uses
+License: GPL-3
 Encoding: UTF-8
 LazyData: true
+Imports: 
+    tidyverse
+    crayon
+    clisymbols
+    impute
+    reshape2
 Suggests: 
     covr,
-    testthat (>= 2.1.0),
-    tidyverse
+    testthat (>= 2.1.0)
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 6.1.1

R/PomaImpute.R

@@ -5,6 +5,14 @@ PomaImpute <- function(data,
                        cutoff = 20,
                        method = c("none", "half_min", "median", "mean", "min", "knn")){
 
+  if (!(method %in% c("none", "half_min", "median", "mean", "min", "knn"))) {
+    stop(crayon::red(clisymbols::symbol$cross, "Incorrect value for method argument!"))
+  }
+  if (missing(method)) {
+    method <- "knn"
+    warning("method argument is empty! KNN will be used")
+  }
+
   data <- as.data.frame(data)
   samples_groups <- data[, 1:2]
   to_imp_data <- data[, c(3:ncol(data))]

R/PomaNormPlot.R

@@ -0,0 +1,55 @@
+
+PomaNormPlot <- function(data, group = c("subjects", "metabolites")){
+
+  if (missing(group)) {
+    group <- "subjects"
+    warning("group argument is empty! subjects will be used")
+  }
+
+  colnames(data)[1:2] <- c("ID", "Group")
+  data <- data %>% mutate(ID = paste0(row_number(), "_", ID))
+
+  normtable_metabolites <- select(data, -ID) %>%
+    reshape2::melt()
+
+  normtable_subjects <- select(data, -Group) %>%
+    as_tibble() %>%
+    gather(var, value, -ID) %>%
+    spread(ID, value) %>%
+    reshape2::melt()
+
+  normtable_subjects <- normtable_subjects %>%
+    mutate(variable = str_replace_all(variable, "._", ""))
+
+  if(group == "subjects"){
+
+    normtable_subjects %>%
+      group_by(variable) %>%
+      ggplot(aes(variable, value, color = variable)) +
+      geom_boxplot() +
+      geom_jitter() +
+      theme(legend.position = "none") +
+      theme_minimal() +
+      xlab("") +
+      ggtitle("Normalization Plot by Subjects") +
+      theme(axis.text.x = element_text(angle = 45, hjust = 1),
+            legend.position = "none")
+
+  }
+  else{
+
+    normtable_metabolites %>%
+      group_by(Group) %>%
+      ggplot(aes(variable, value, color = Group)) +
+      geom_boxplot() +
+      geom_jitter() +
+      theme(legend.position = "none") +
+      theme_minimal() +
+      xlab("") +
+      ggtitle("Normalization Plot by Metabolites") +
+      theme(axis.text.x = element_text(angle = 45, hjust = 1))
+
+  }
+
+}
+

R/PomaUnivariate.R

@@ -6,6 +6,18 @@ PomaUnivariate <- function(data_uni,
                            var_equal = FALSE,
                            adjust = c("fdr", "holm", "hochberg", "hommel", "bonferroni", "BH", "BY")){
 
+  if (missing(method)) {
+    stop(crayon::red(clisymbols::symbol$cross, "Select a method!"))
+  }
+  if (!(method %in% c("ttest", "anova", "mann", "kruskal"))) {
+    stop(crayon::red(clisymbols::symbol$cross, "Incorrect value for method argument!"))
+  }
+  if (missing(adjust)) {
+    adjust <- "fdr"
+    warning("adjust argument is empty! FDR will be used")
+  }
+
+
   colnames(data_uni)[1:2] <- c("ID", "Group")
   Group <- data_uni$Group
 

R/PomaVolcano.R

@@ -5,6 +5,14 @@ PomaVolcano <- function(data,
                         FC_cutoff = 1.5,
                         xlim = 2){
 
+  if (missing(pval)) {
+    pval <- "raw"
+    warning("pval argument is empty! Raw p-value will be used")
+  }
+  if (!(pval %in% c("raw", "adjusted"))) {
+    stop(crayon::red(clisymbols::symbol$cross, "Incorrect value for pval argument!"))
+  }
+
   names <- rownames(data)
 
   if(pval == "raw"){
@@ -26,15 +34,17 @@ PomaVolcano <- function(data,
   ggplot(data = df, aes(x = log2(FC), y = -log10(P.Value), colour = threshold)) +
     geom_point(size=1.75) +
     xlim(c(-(xlim), xlim)) +
-    xlab("log2 fold change") + ylab("-log10 p-value")+
+    xlab("log2 fold change") +
+    ylab("-log10 p-value") +
     scale_y_continuous(trans = "log1p")+
     ggtitle("Comparisson: Group2/Group1") +
-    geom_label(data = df[df$P.Value < Pval_cutoff & (df$FC > FC_cutoff | log2(df$FC) < -log2(FC_cutoff)),],
-              aes(x = log2(FC), y = -log10(P.Value)+0.12, label = names), show.legend = FALSE) +
+    ggrepel::geom_label_repel(data = df[df$P.Value < Pval_cutoff & (df$FC > FC_cutoff | log2(df$FC) < -log2(FC_cutoff)),],
+              aes(x = log2(FC), y = -log10(P.Value), label = names), show.legend = FALSE) +
     geom_vline(xintercept = -log2(FC_cutoff), colour = "black") +
     geom_vline(xintercept = log2(FC_cutoff), colour = "black") +
     geom_hline(yintercept = -log10(Pval_cutoff), colour = "black") +
-    theme(legend.position = "none")+ theme_minimal() +
+    theme(legend.position = "none") +
+    theme_minimal() +
     scale_color_manual(values = c("Down-regulated" = "#E64B35", "Up-regulated" = "#3182bd", "none" = "#636363"))
 
   }

README.md

@@ -1,5 +1,7 @@
 # POMA package
 
+## R Package for Statistical Analysis of Metabolomic Data
+
   <!-- badges: start -->
   [![Codecov test coverage](https://codecov.io/gh/pcastellanoescuder/POMA_package/branch/master/graph/badge.svg)](https://codecov.io/gh/pcastellanoescuder/POMA_package?branch=master)
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