bars_fun, heatmap_fun

bars_fun: add ylab argument
heatmap: add feature to use preformated phyloseq object, add table output that can be used to create boxplot with specific taxa with normalized abundances.

R/ASVenn_fun.R

@@ -82,8 +82,8 @@ ASVenn_fun <- function(data = data, output = "./ASVenn/", rank = "ASV",
   if(length(lvls)==0){
     flog.error('You must provide levels...')
     stop()
-  } else if(length(lvls)>5){
-    flog.error('Venn diagram is limited to 5 levels')
+  } else if(length(lvls)>7){
+    flog.error('Venn diagram is limited to 7 levels')
     stop()
   } else{
     if(!all(lvls %in% na.omit(levels(as.factor(sample_data(data)[,column1]@.Data[[1]])) ))){
@@ -93,19 +93,6 @@ ASVenn_fun <- function(data = data, output = "./ASVenn/", rank = "ASV",
   }
 
 
-  if(length(lvls)==0){
-    flog.error('You must provide levels...')
-    stop()
-  } else if(length(lvls)>5){
-    flog.error('Venn diagram is limited to 5 levels')
-    stop()
-  } else{
-    if(!all(lvls %in% na.omit(levels(as.factor(sample_data(data)[,column1]@.Data[[1]])) ))){
-      flog.error('Your levels are not present in metadata...')
-      stop()
-    }
-  }
-
 
   #Nombre d'espèce par matrice
   flog.info('Parsing factor ...')

R/bars_fun.R

@@ -41,6 +41,7 @@ rarefaction <- function(data = data, col = NULL, step = 100, ggplotly = TRUE){
 #' @param Fact1 Variable used to change X axis tick labels and color (when split = FALSE)
 #' @param split if TRUE make a facet_wrap like grouped by Ord1 (default FALSE)
 #' @param relative Plot relative (TRUE, default) or raw abundance plot (FALSE)
+#' @param ylab Y axis title ("Abundance")
 #' @param outfile Output html file.
 #'
 #' @return Returns barplots in an interactive plotly community plot
@@ -56,8 +57,7 @@ rarefaction <- function(data = data, col = NULL, step = 100, ggplotly = TRUE){
 
 
 bars_fun <- function(data = data, rank = "Genus", top = 10, Ord1 = NULL, Fact1 = NULL, split = FALSE,
-                     relative = TRUE,
-                     outfile="plot_compo.html", verbose = TRUE){
+                     relative = TRUE, ylab = "Abundance", outfile="plot_compo.html", verbose = TRUE){
 
   if(verbose){
     invisible(flog.threshold(INFO))
@@ -125,13 +125,12 @@ if( all(Ord1 != sample_variables(data)) | all(Fact1 != sample_variables(data))){
     legendgroup = ~g,
     showlegend = FALSE
   ) %>% layout(xaxis = list(zeroline = FALSE,showline = FALSE, showgrid = FALSE),
-               yaxis=list(showticklabels = FALSE,title = "",showgrid = FALSE))
+               yaxis=list(showticklabels = FALSE,title = ylab, showgrid = FALSE))
 
 
   if(relative){
   flog.info('Plotting relative...')
     #relative abondance
-    plottitle = "Relative abundance"
     otable=apply(otable,2, function(x){Tot=sum(x); x/Tot})
     dat= as.data.frame(t(otable))
     dat <- cbind.data.frame(sdata, dat)
@@ -143,7 +142,7 @@ if( all(Ord1 != sample_variables(data)) | all(Fact1 != sample_variables(data))){
     eval(parse(text=fun))
 
     p1=plot_ly(meltdat, x = ~sample.id, y = ~value, type = 'bar', name = ~variable, color = ~variable) %>% #, color = ~variable
-      layout(title="Relative abundance", yaxis = list(title = 'Relative abundance'), xaxis = xform, barmode = 'stack')
+      layout(title="", yaxis = list(title = ylab), xaxis = xform, barmode = 'stack')
 
     if(length(df1$x) != length(unique(df1$g))){
       p1 <- subplot(p1, subp1, nrows = 2, shareX = T, heights=c(0.95,0.05)) %>%
@@ -152,9 +151,8 @@ if( all(Ord1 != sample_variables(data)) | all(Fact1 != sample_variables(data))){
   }else{
   flog.info('Plotting raw...')
     #raw abundance
-    plottitle = "Raw abundance"
     p1=plot_ly(meltdat, x = ~sample.id, y = ~value, type = 'bar', name = ~variable, color = ~variable) %>% #, color = ~variable
-      layout(title="Raw abundance", yaxis = list(title = 'Raw abundance'), xaxis = xform, barmode = 'stack')
+      layout(title="", yaxis = list(title = ylab), xaxis = xform, barmode = 'stack')
 
     if(length(df1$x) != length(unique(df1$g))){
       p1 <- subplot(p1, subp1, nrows = 2, shareX = T, heights=c(0.95,0.05)) %>%
@@ -178,9 +176,9 @@ if( all(Ord1 != sample_variables(data)) | all(Fact1 != sample_variables(data))){
                                  showlegend = (.y == levels(meltdat[, Ord1])[1])),
                        keep = TRUE)  %>%
       subplot(nrows = 1, shareX = TRUE, shareY=TRUE, titleX = FALSE) %>%
-      layout(title=plottitle,
+      layout(title="",
              xaxis = list(title = glue("{Ord1} = {unique(meltdat[, Ord1])[1]}")),
-             yaxis = list(title = 'Relative abundance'),
+             yaxis = list(title = ylab),
              barmode = 'stack')
 
     for (i in 2:length(unique(meltdat[, Ord1]))) {

R/heatmap_fun.R

@@ -6,7 +6,10 @@
 #' @param output Output directory
 #' @param column1 Column name of factor to plot with (among sample_variables(data)).
 #' @param top Number of top features to plot.
+#' @param relative If TRUE, calculate relative abundance, needs a phyloseq object with raw abundance.
+#' @param aggregate If TRUE, aggregate abundance of non "top" taxa in a new taxa named "Other".
 #' @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 legend Legend title ("Abundance")
 #'
 #' @return Generate an heatmap with top taxa (html plotly version in output directory)
 #' @importFrom htmlwidgets saveWidget
@@ -16,7 +19,8 @@
 
 # Decontam Function
 
-heatmap_fun <- function(data = data, column1 = "", top = 20, output = "./plot_heatmap/", rank = "Species"){
+heatmap_fun <- function(data = data, column1 = "", top = 20, output = "./plot_heatmap/", rank = "Species", relative = TRUE, aggregate = TRUE, legend = "Abundance"){
+  LL = list()
 
   output1 <- paste(getwd(),'/',output,'/',sep='')
   if(!dir.exists(output1)){
@@ -24,16 +28,37 @@ heatmap_fun <- function(data = data, column1 = "", top = 20, output = "./plot_he
   }
   flog.info('Done.')
 
-  psobj.top <- microbiome::aggregate_top_taxa(data, rank, top = top)
+  ps.glom.rel <- psobj.top <- dataglom <- data
 
-  ps.glom.rel <- microbiome::transform(psobj.top, "compositional")
+  if(!is.null(rank)){
+    dataglom <- tax_glom(data, rank)
+    tt <- tax_table(dataglom)
+    taxa <- tt[,rank]
+    taxa_names(dataglom) <- taxa
+  }
+
+  otable <- otu_table(dataglom)
+  sdata <- as.data.frame(as.matrix(sample_data(dataglom)))
 
+  data.com <- reshape2::melt(otable)
+  data.com$xlabel <- as.factor(sdata[as.character(data.com$Var2),match(column1,names(sdata))])
+  names(data.com) <- c("Tax", "Sample", "Abundance", "xlabel")
+  data.com$Tax = factor(data.com$Tax, levels = sort(unique(as.character(data.com$Tax))))
+
+  if(aggregate){psobj.top <- microbiome::aggregate_top_taxa(data, rank, top = top)}
+
+  if(relative){
+    ps.glom.rel <- microbiome::transform(psobj.top, "compositional")
     plot.composition.relAbun <- microbiome::plot_composition(ps.glom.rel, x.label = column1)
     data.com <- plot.composition.relAbun$data
     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("Relative\nabundance", palette = "RdYlBu") + theme_bw()
+  p.heat <- p.heat + scale_fill_distiller(legend, palette = "RdYlBu") + theme_bw()
 
   # Make bacterial names italics
   p.heat <- p.heat + theme(axis.text.y = element_text(colour = 'black',
@@ -57,5 +82,8 @@ heatmap_fun <- function(data = data, column1 = "", top = 20, output = "./plot_he
   flog.info(paste(output1,"heatmap_",column1,".html",sep=''))
   saveWidget(pltly.heat, file=  paste(output1,"heatmap_",column1,".html",sep=''))
 
-  return(p.heat)
+
+  LL$plot <- p.heat
+  LL$table <- data.com
+  return(LL)
 }

man/bars_fun.Rd

@@ -12,7 +12,9 @@ bars_fun(
   Fact1 = NULL,
   split = FALSE,
   relative = TRUE,
-  outfile = "plot_compo.html"
+  ylab = "Abundance",
+  outfile = "plot_compo.html",
+  verbose = TRUE
 )
 }
 \arguments{
@@ -30,6 +32,8 @@ bars_fun(
 
 \item{relative}{Plot relative (TRUE, default) or raw abundance plot (FALSE)}
 
+\item{ylab}{Y axis title ("Abundance")}
+
 \item{outfile}{Output html file.}
 }
 \value{

man/heatmap_fun.Rd

@@ -9,7 +9,10 @@ heatmap_fun(
   column1 = "",
   top = 20,
   output = "./plot_heatmap/",
-  rank = "Species"
+  rank = "Species",
+  relative = TRUE,
+  aggregate = TRUE,
+  legend = "Abundance"
 )
 }
 \arguments{
@@ -22,6 +25,12 @@ heatmap_fun(
 \item{output}{Output directory}
 
 \item{rank}{Taxonomy rank to merge features that have same taxonomy at a certain taxonomic rank (among rank_names(data), or 'ASV' for no glom)}
+
+\item{relative}{If TRUE, calculate relative abundance, needs a phyloseq object with raw abundance.}
+
+\item{aggregate}{If TRUE, aggregate abundance of non "top" taxa in a new taxa named "Other".}
+
+\item{legend}{Legend title ("Abundance")}
 }
 \value{
 Generate an heatmap with top taxa (html plotly version in output directory)