Commit 7acdfd87 authored by Etienne Rifa's avatar Etienne Rifa
Browse files

fix alpha indices output

parents fde545de 3f05a693
Pipeline #43024 passed with stage
in 12 seconds
......@@ -107,9 +107,6 @@ diversity_alpha_fun <- function(data = data, output = "./plot_div_alpha/", colum
resAlpha = list()
flog.info('Alpha diversity tab ...')
# row.names(resAlpha$alphatable) <- gsub("X","",row.names(resAlpha$alphatable))
write.table(resAlpha$alphatable,paste(output,'/alphaDiversity_table.csv',sep=''), sep="\t", row.names=TRUE, col.names=NA, quote=FALSE)
flog.info('Done.')
p <- alphaPlot(data, column1, column2, measures)
......@@ -120,6 +117,10 @@ diversity_alpha_fun <- function(data = data, output = "./plot_div_alpha/", colum
anova_data <- cbind(sample_data(data), alphatable)
anova_data$Depth <- sample_sums(data)
resAlpha$alphatable <- anova_data
# row.names(resAlpha$alphatable) <- gsub("X","",row.names(resAlpha$alphatable))
write.table(resAlpha$alphatable,paste(output,'/alphaDiversity_table.csv',sep=''), sep="\t", row.names=TRUE, col.names=NA, quote=FALSE)
flog.info('Done.')
if(length(levels(as.factor(anova_data[,column1])))>1 & mean(table(anova_data[,column1])) != 1 ){
flog.info('ANOVA ...')
# variables <- paste(sep=" + ", "Depth", var1)
......
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