otu_heatmap: Create a heatmap of OTU counts.

In qiimer: Work with QIIME Output Files in R

Description

Create a heatmap of OTU counts.

Usage

otu_heatmap(otu_counts, assignments, threshold = 0, plot = T,
  color = saturated_rainbow(100), breaks = c(0, 1e-10, seq(0.001, 1,
  length.out = 100)), ...)

Arguments

otu_counts	A matrix of OTU counts, one row per OTU and one column per sample.
assignments	A character vector of OTU assignments. Length should match number of rows in otu_counts.
threshold	Minimum number of OTU counts necessary for an assignment to be included in the heatmap. Assignments are filtered after calculating the proportions, so the threshold setting does not affect the display of the remaining OTUs.
plot	If true, display a plot. If false, just return the computed abundances.
color	Vector of colors to use in the heatmap.
breaks	Vector of color breaks, one element greater in length than 'colors'.
...	Additional arguments are passed to the pheatmap function.

Value

A heatmap plot of the proportions of assignments in each sample, and invisibly returns a matrix of the proportions in the plot.

See Also

saturated_rainbow

Examples

data(relmbeta_assignments)
data(relmbeta_counts)
a <- simplify_assignments(split_assignments(relmbeta_assignments))

## Not run: 
otu_heatmap(relmbeta_counts, a, threshold=10)
otu_heatmap(
  relmbeta_counts, a, threshold=10, 
  cluster_rows=FALSE, cluster_cols=FALSE, 
  cellwidth=12, cellheight=12)

## End(Not run)

heatmap_data <- otu_heatmap(relmbeta_counts, a, threshold=10, plot=FALSE)
head(heatmap_data)

Example output

                               A1    A2    A3    A4    A5    B1    B2    B3
Bacteria                    0.128 0.110 0.090 0.072 0.132 0.084 0.060 0.112
Bacteroidetes               0.686 0.692 0.704 0.700 0.552 0.356 0.556 0.652
Bacteroidetes Alistipes     0.054 0.022 0.066 0.048 0.112 0.100 0.030 0.038
Bacteroidetes Bacteroidales 0.018 0.020 0.024 0.024 0.010 0.034 0.072 0.030
Bacteroidetes Bacteroides   0.030 0.018 0.026 0.024 0.018 0.140 0.154 0.050
Bacteroidetes Odoribacter   0.000 0.010 0.004 0.000 0.012 0.002 0.002 0.020
                               B4    B5    C1    C2    C3    C4    C5    D1
Bacteria                    0.080 0.076 0.176 0.144 0.188 0.074 0.030 0.212
Bacteroidetes               0.674 0.584 0.380 0.132 0.236 0.016 0.110 0.222
Bacteroidetes Alistipes     0.036 0.064 0.038 0.042 0.032 0.014 0.160 0.012
Bacteroidetes Bacteroidales 0.046 0.056 0.000 0.000 0.000 0.000 0.000 0.000
Bacteroidetes Bacteroides   0.050 0.098 0.098 0.006 0.050 0.004 0.048 0.090
Bacteroidetes Odoribacter   0.008 0.004 0.000 0.000 0.000 0.000 0.002 0.002
                               D2    D3    D4    D5
Bacteria                    0.124 0.086 0.148 0.168
Bacteroidetes               0.154 0.136 0.336 0.232
Bacteroidetes Alistipes     0.014 0.016 0.034 0.048
Bacteroidetes Bacteroidales 0.000 0.000 0.000 0.000
Bacteroidetes Bacteroides   0.008 0.016 0.034 0.028
Bacteroidetes Odoribacter   0.000 0.000 0.000 0.000

qiimer documentation built on May 2, 2019, 6 a.m.