In microbiome/HITChipDB: HITChipDB

Oligoprofile heatmap

Reproduce and modify the oligo heatmap of the run.profiling.script. Plots heatmap of the oligo profiles together with phylotype groups and sample clusters. Reload and plot preprocessed data from the run.profiling.script by using the read.profiling function, assuming you have stored the output in directory "datadirectory/". Start by reading the data:

library(microbiome)
library(HITChipDB)

# Define data directory (here: simulated data directory)
data.directory <- system.file("extdata", package = "microbiome")

# Read Oligo level data in original domain
probedata <- read_hitchip(data.directory, "frpa")$probedata

# Read Oligo-phylogeny mapping table (two methods):
taxonomy <- GetPhylogeny("HITChip", "filtered")

Save the image in a file (too large to be opened directly in R). To prevent ordering of the rows, use hclust.method = NULL in the function call:

library(microbiome)
ppcm <- 150
png(filename = "oligoprofileClustering.png", 
     width = max(trunc(ppcm*21), 
                 trunc(ppcm*21*ncol(probedata)/70)), 
     height = trunc(ppcm*29.7))
tmp <- PlotPhylochipHeatmap(probedata, 
        taxonomy, level = "L1", metric = "pearson")
dev.off()