Barplots
The following example picks 20 random species from a species data vector and visualizes them as ordered barplot colored according to the L2 group. Here with simulated example data. See read.profiling to use your own data files.
library(microbiome, quietly = TRUE)
# Microbiota profiling data. Read as: bacteria x samples matrix
data(peerj32) # From https://peerj.com/articles/32/
l2.log10.simulated <- t(peerj32$microbes)
# Pick example data and visualize
x <- l2.log10.simulated[,1]
phylogeny.info <- GetPhylogeny("HITChip")
p <- phylo.barplot(x, color.level = "L1", title = "My title", phylogeny.info = phylogeny.info)The following example picks 20 random species and visualizes the HITChip signal as ordered barplot. In this example the bars are colored according to the L2 group.
# Load Phylogeny
phylogeny.info <- GetPhylogeny("HITChip")
# Get example data
data.directory <- system.file("extdata", package = "microbiome")
species.log10.simulated <- read.profiling(level = "species", method = "frpa", data.dir = data.directory, log10 = TRUE)
# Pick 20 species from first sample at random
taxa <- rownames(species.log10.simulated)[sample(nrow(species.log10.simulated), 20)]
# Signal of the selected taxa at first sample
signal <- species.log10.simulated[taxa,1]
# Higher-level taxonomic groups for the taxa
l2 <- droplevels(levelmap(taxa, level.from = "taxa", level.to = "L2", phylogeny.info = phylogeny.info)$L2)## Error in droplevels(levelmap(taxa, level.from = "taxa", level.to = "L2", : error in evaluating the argument 'x' in selecting a method for function 'droplevels': Error in levelmap(taxa, level.from = "taxa", level.to = "L2", phylogeny.info = phylogeny.info) :
## object 'sl' not found
l1 <- droplevels(levelmap(taxa, level.from = "taxa", level.to = "L1", phylogeny.info = phylogeny.info)$L1)## Error in droplevels(levelmap(taxa, level.from = "taxa", level.to = "L1", : error in evaluating the argument 'x' in selecting a method for function 'droplevels': Error in levelmap(taxa, level.from = "taxa", level.to = "L1", phylogeny.info = phylogeny.info) :
## object 'sl' not found
# Collect all into a data.frame
df <- list()
df$taxa <- taxa
df$L2 <- l2## Error in eval(expr, envir, enclos): object 'l2' not found
df$L1 <- l1## Error in eval(expr, envir, enclos): object 'l1' not found
df$signal <- signal
df <- data.frame(df)
# Define colors for L1/L2 groups
l2.colors <- rainbow(length(unique(df$L2)))
names(l2.colors) <- as.character(unique(df$L2))
l1.colors <- rainbow(length(unique(df$L1)))
names(l1.colors) <- as.character(unique(df$L1))
# Rearrange the data.frame
m <- melt(df)
# Sort by signal (ie. change order of factors for plot)
df <- within(df, taxa <- factor(taxa, levels = taxa[order(abs(signal))]))
# Plot the image
p <- ggplot(aes(x = taxa, y = signal, fill = L2), data = df) ## Error in eval(expr, envir, enclos): could not find function "ggplot"
p <- p + scale_fill_manual(values = l2.colors[as.character(levels(df$L2))])## Error in eval(expr, envir, enclos): could not find function "scale_fill_manual"
p <- p + geom_bar(position="identity", stat = "identity") + theme_bw() + coord_flip()## Error in eval(expr, envir, enclos): could not find function "geom_bar"
p <- p + ylab("Fold change") + xlab("") + ggtitle("My barplot")## Error in eval(expr, envir, enclos): could not find function "ylab"
p <- p + theme(legend.position="right")## Error in eval(expr, envir, enclos): could not find function "theme"
p <- p + theme(panel.border=element_rect())## Error in eval(expr, envir, enclos): could not find function "theme"
print(p)