more outputs + infos for beta + misc changes

R/diversity_beta_light.R

@@ -5,7 +5,7 @@
 #' @param psobj a phyloseq object (output from decontam or generate_phyloseq)
 #' @param rank Taxonomy rank to merge features that have same taxonomy at a certain taxonomic rank (among rank_names(data), or 'ASV' for no glom)
 #' @param col A metadata column (among sample_variables(data)).
-#' @param cov Covariable names comma separated vector.
+#' @param cov Covariable names comma separated vector (last covariable is used to plot samples with different shape).
 #' @param dist0 Dissimilarity index, partial match to "unifrac", "wunifrac", "dpcoa", "jsd", "manhattan", "euclidean", "canberra", "bray", "kulczynski", "jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup" , "binomial", "chao", "cao" or "mahalanobis".
 #' @param ord0 Currently supported method options are: c("DCA", "CCA", "RDA", "CAP", "DPCoA", "NMDS", "MDS", "PCoA")
 #' @param output The output file directory.
@@ -34,50 +34,48 @@ diversity_beta_light <- function(psobj, rank = "ASV", col = NULL, cov = NULL, di
 
   flog.debug(cov)
   if(!is.null(cov)){
-    cov1 = unlist(strsplit(cov, ","))
+    cov1 <- unlist(strsplit(cov, ","))
   }
 
-  # metrics <- sapply(strsplit(measures,","), '[')
-  col1 = unlist(strsplit(col, "[+]"))
+  col1 <- col
   if(length(col1)==1){
     fun <- paste("psobj = subset_samples(psobj, !is.na(",col,"))",sep="")
     eval(parse(text=fun))
   }else{
-    fun <- paste("psobj = subset_samples(psobj, !is.na(",col1[1],"))",sep="")
-    eval(parse(text=fun))
-    fun <- paste("psobj = subset_samples(psobj, !is.na(",col1[2],"))",sep="")
-    eval(parse(text=fun))
-  }
+    stop("Only one factor in 'col' argument, add more covariable in 'cov' argument.")
+    }
+
   if(rank=="ASV"){
     flog.info('No glom ...')
-    data_rank = psobj
+    data_rank <- psobj
   }else{
-    data_rank = tax_glom(psobj, rank)
+    data_rank <- tax_glom(psobj, rank)
   }
 
 
   # Figure
-  resBeta = list()
+  flog.info('Plot ...')
+  resBeta <- list()
   if(!is.null(cov)){
-  p1 <- plot_samples(data_rank, ordinate(data_rank, ord0, dist0), color = col, shape = cov1[1] ) +
+  p1 <- plot_samples(data_rank, ordinate(data_rank, ord0, dist0), color = col, shape = cov1[length(cov1)] ) +
   theme_bw() + ggtitle(glue::glue("{ord0} + {dist0}")) + stat_ellipse() + scale_shape_manual(values = 0:10)
 }else{
   p1 <- plot_samples(data_rank, ordinate(data_rank, ord0, dist0), color = col) +
   theme_bw() + ggtitle(glue::glue("{ord0} + {dist0}")) + stat_ellipse()
 }
   # plot(p1)
-
-  resBeta$plot = p1 + theme(axis.text.x = element_text(angle = 45, hjust=1),
+  flog.info('Plot ok...')
+  resBeta$plot <- p1 + theme(axis.text.x = element_text(angle = 45, hjust=1),
   ,axis.text=element_text(size=18),
   axis.title=element_text(size=16,face="bold"),
   strip.text.x = element_text(size = 18,face="bold"),
   title=element_text(size=16,face="bold"))
 
   if(tests){
-    otable = otu_table(data_rank)
+    otable <- otu_table(data_rank)
 
     flog.info(glue::glue('Tests on {dist0} ...'))
-    mdata = data.frame(sample_data(data_rank))
+    mdata <- data.frame(sample_data(data_rank))
     mdata$Depth <- sample_sums(data_rank)
     if( any(grepl(dist0, c("unifrac", "wunifrac", "dpcoa", "jsd") )) ){
       dist1 <-phyloseq::distance(data_rank, dist0)
@@ -85,18 +83,21 @@ diversity_beta_light <- function(psobj, rank = "ASV", col = NULL, cov = NULL, di
       dist1 <<- vegdist(t(otable), method = dist0)
     }
     if(!is.null(cov)){
-      resBC = adonis(as.formula(paste('dist1 ~ Depth +', paste(cov1, collapse="+"), "+", col)), data = mdata, permutations = 1000)
+      form1 <- as.formula(paste('dist1 ~ Depth +', paste(cov1, collapse="+"), "+", col))
+      resBC <- adonis(form1, data = mdata, permutations = 1000)
+        
     }else{
-      resBC = adonis(as.formula(paste('dist1 ~ Depth +', col)), data = mdata, permutations = 1000)
+      form1 <- as.formula(paste('dist1 ~ Depth +', col))
+      resBC <- adonis(form1, data = mdata, permutations = 1000)
     }
 
     #PairwiseAdonis
     # resBC2 = pairwise.adonis2(as.formula( paste('BC.dist ~ ', col,sep="") ), data = mdata)
     if(length(col1)>1){
       fact1 <- apply( mdata[,c(col1)] , 1 , paste , collapse = "-" )
-      resBC2 = pairwise.adonis(dist1, fact1, p.adjust.m='fdr')
+      resBC2 <- pairwise.adonis(dist1, fact1, p.adjust.m='fdr')
     } else {
-      resBC2 = pairwise.adonis(dist1, mdata[,c(col1)], p.adjust.m='fdr')
+      resBC2 <- pairwise.adonis(dist1, mdata[,c(col1)], p.adjust.m='fdr')
     }
 
     write.table(resBC$aov.tab, file=paste0(output,'/',col,'_permANOVA.txt'), sep="\t")
@@ -104,9 +105,12 @@ diversity_beta_light <- function(psobj, rank = "ASV", col = NULL, cov = NULL, di
 
     ggsave(glue::glue("{output}/beta_diversity.eps"), plot=resBeta$plot, height = 20, width = 30, units="cm", dpi = 500, device="eps")
 
-    resBeta$permanova = resBC$aov.tab
-    resBeta$pairwisepermanova = resBC2
+    resBeta$permanova <- resBC$aov.tab
+    resBeta$permanova_formula <- format(form1)
+    resBeta$pairwisepermanova <- resBC2
+    resBeta$test_table <- mdata
+    resBeta$dist <- dist1
 
   }
   return(resBeta)
-}
+}
\ No newline at end of file

R/heatmap_fun.R

@@ -20,7 +20,7 @@ heatmap_fun <- function(data = data, column1 = "", top = 20, output = "./plot_he
 
   output1 <- paste(getwd(),'/',output,'/',sep='')
   if(!dir.exists(output1)){
-    dir.create(output1)
+    dir.create(output1, recursive = TRUE)
   }
   flog.info('Done.')
 
@@ -33,7 +33,7 @@ heatmap_fun <- function(data = data, column1 = "", top = 20, output = "./plot_he
   colnames(data.com)
 
   p.heat <- ggplot(data.com, aes(x = Sample, y = Tax)) + geom_tile(aes(fill = Abundance))
-  p.heat <- p.heat + scale_fill_distiller("Abundance", palette = "RdYlBu") + theme_bw()
+  p.heat <- p.heat + scale_fill_distiller("Relative\nabundance", palette = "RdYlBu") + theme_bw()
 
   # Make bacterial names italics
   p.heat <- p.heat + theme(axis.text.y = element_text(colour = 'black',

man/ASVenn_fun.Rd

@@ -12,7 +12,9 @@ ASVenn_fun(
   subset = "",
   lvls = NULL,
   krona = "",
-  shared = TRUE
+  shared = TRUE,
+  verbose = 2,
+  ggplotmode = FALSE
 )
 }
 \arguments{
@@ -31,6 +33,10 @@ ASVenn_fun(
 \item{krona}{Krona of exclusive ASV or shared with informed level and others. Must be among levels of column1 argument.}
 
 \item{shared}{shared [TRUE] or exclusive [FALSE] mode.}
+
+\item{verbose}{Verbose level. (1: quiet, 2: print infos, 3: print infos + debug)}
+
+\item{ggplotmode}{if TRUE plot the Venn diagram using ggplot}
 }
 \value{
 Returns list with venn diagram and table with shared features. Exports a venn diagram with corresponding tabulated file.

man/VENNFUN.Rd

@@ -10,7 +10,8 @@ VENNFUN(
   TITRE = TITRE,
   output = "./",
   refseq1 = NULL,
-  alltax = NULL
+  alltax = NULL,
+  ggplotmode = FALSE
 )
 }
 \arguments{
@@ -25,6 +26,8 @@ VENNFUN(
 \item{refseq1}{Reference sequences.}
 
 \item{alltax}{Taxonomy table.}
+
+\item{ggplotmode}{if TRUE plot the Venn diagram using ggplot}
 }
 \value{
 Exports a venn diagram with corresponding tabulated file.

man/diversity_beta_light.Rd

@@ -22,7 +22,7 @@ diversity_beta_light(
 
 \item{col}{A metadata column (among sample_variables(data)).}
 
-\item{cov}{Covariable names comma separated vector.}
+\item{cov}{Covariable names comma separated vector (last covariable is used to plot samples with different shape).}
 
 \item{dist0}{Dissimilarity index, partial match to "unifrac", "wunifrac", "dpcoa", "jsd", "manhattan", "euclidean", "canberra", "bray", "kulczynski", "jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup" , "binomial", "chao", "cao" or "mahalanobis".}