Embedded Files
Con R podemos también visualizar los resultados. El script mg_classifier en sus últimas versiones (v1.7.7) genera un archivo (families_plot.csv) con las 15 familias más abundantes listas para ser graficadas con un script en R, ya probado en R Studio.
El archivo families_plot.csv tiene la siguiente estructura, la primer línea es un comentario, por eso empieza con #
# Only the 15 most abundant familiesphylum-family,F3D0,F3D150,F3D9,MockBacteroidetes-S24-7_f,3813,3086,2575,10Firmicutes-Lachnospiraceae,2143,1305,2124,2Bacteroidetes-Bacteroidaceae,189,216,686,274Firmicutes-Ruminococcaceae,477,203,483,0Bacteroidetes-Rikenellaceae,198,138,490,0Firmicutes-Lactobacillaceae,123,157,256,141Firmicutes-Staphylococcaceae,0,0,0,628Firmicutes-Streptococcaceae,5,0,0,492Firmicutes-Clostridiaceae,132,7,0,310Proteobacteria-Moraxellaceae,0,0,0,412Firmicutes-Bacillaceae,0,0,0,389Actinobacteria-Actinomycetaceae,0,0,0,366Proteobacteria-Helicobacteraceae,0,0,0,363Proteobacteria-Neisseriaceae,0,0,0,305Proteobacteria-Enterobacteriaceae,6,0,2,200El script families_plot.r puedes copiar y pegarlo en un archivo o bien descargarlo de aquí
# To be used with the families_plot.csv file produced by mg_classifier.v1.7.7# Import csv with headingsfamilies_plot <- read.csv("families_plot.csv")leyenda <- (families_plot$phylum.family) # gets the data for the legendmymat <- t(families_plot[-1]) # convert table to matrix except column 1data_percentage=apply(t(mymat), 2, function(x){x*100/sum(x,na.rm=T)}) # calculates the percentageslibrary(RColorBrewer) # library for color palletscoul = brewer.pal(12, "Set3") #12 color palletebarplot( data_percentage, main = "Family", family = "mono", #AXES FORMAT las = 2, # sample name rotated ylab = "percentage", # y axis label #xlim = c(0, 35), # reduces the width of the x axis cex.axis = 1, # font size of y axis cex.names = 0.8, # font of the bar labels (x) # LEGEND legend.text = leyenda, # legend from the variable above args.legend = list(x = "right", cex = 1, title ="Phylum-Family"), # PALLET col=coul) # color palletPhyla
Phyla
También tenemos scripts para graficar con R o R-Studio, los datos de los archivos con número de phyla.
phyla15plot.r
phyla15plot.r
# To be used with the phyla15_plot file produced by mg_classifier.v1.7.7# Import with headingsleyenda <- (phyla15_plot$phylum) # gets the data for the legend, row 1mymat <- t(phyla15_plot[-1]) # convert table to matrix except column 1data_percentage=apply(t(mymat), 2, function(x){x*100/sum(x,na.rm=T)}) # calculates the percentagespar(mar = c(6, 4, 4, 2) + 0.1) # set bottom margin to a higher valuebarplot( data_percentage, main = "95% of phyla", family = "mono", #AXES FORMAT #las = 2, # sample name rotated ylab = "percentage", # y axis label xlim = c(0, 6.5), # reduces the width of the x axis, higher value shorter x cex.axis = 1.1, # font size of y axis cex.names = 1.1, # font of the bar labels (x) # LEGEND legend.text = leyenda, # legend from the variable above args.legend = list(x = "right", cex = 1.2, title ="Phylum", ncol = 1, inset = 0, xpd=TRUE), # args.legend = list(x = "right", ncol = 1, cex = 1.3, inset = 0, xpd=TRUE), # COLOR PALLET col=c("#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F", "#FF9864", "#9997FC", "#9C9C9C")) # end of plot# Jugar con xlim e inset para ajustar el tamano del grafico y la legenda
phyla_plor.r
phyla_plor.r
#!/usr/bin/env Rscript# To be used with the phyla_plot.csv file produced by mg_classifier.v1.7.9# Import with headingsphyla_plot <- read.csv("phyla_plot.csv", comment.char="#")leyenda <- (phyla_plot$phylum) # gets the data for the legend, row 1mymat <- t(phyla_plot[-1]) # convert table to matrix except column 1data_percentage=apply(t(mymat), 2, function(x){x*100/sum(x,na.rm=T)}) # calculates the percentages# PLOTpng(file="phyla.png",width=2000,height=1600,res=300)barplot( data_percentage, main = "Phyla", family = "mono", cex = 0.6, # BARS width = 1, # width of each bar #AXES FORMAT las = 2, # sample name rotated ylab = "percentage", cex = 0.6, # y axis label xlim = c(1, 40), # reduces the width of the x axis, higher value shorter x cex.axis = 0.6, # font size of y axis cex.names = 0.8, # font of the bar labels (x) # LEGEND legend.text = leyenda, # legend from the variable above args.legend = list(x = "topright", cex = 0.6, title ="Phylum", inset=c(-0.02,0), xpd=TRUE), # COLOR PALLET col=c("#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F", "#FF9864", "#9997FC", "#9C9C9C")) # end of plotdev.off()# Jugar con xlim e inset para ajustar el tamano del grafico y la legendaPage updated
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