plotHeatmap {SQMtools}

Plot a heatmap using ggplot2

Description

Plot a ggplot2 heatmap from a matrix or data frame. The data should be in tabular format (e.g. features in rows and samples in columns).

Usage

plotHeatmap(
  data,
  label_x = "Samples",
  label_y = "Features",
  label_fill = "Abundance",
  gradient_col = c("ghostwhite", "dodgerblue4"),
  base_size = 11,
  metadata_groups = NULL
)

Arguments

data

numeric matrix or data frame.

label_x

character Label for the x axis (default "Samples").

label_y

character Label for the y axis (default "Features").

label_fill

character Label for color scale (default "Abundance").

gradient_col

A vector of two colors representing the low and high ends of the color gradient (default c("ghostwhite", "dodgerblue4")).

base_size

numeric. Base font size (default 11).

metadata_groups

list. Split the plot into groups defined by the user: list('G1' = c('sample1', sample2'), 'G2' = c('sample3', 'sample4')) default NULL).

Value

A ggplot2 plot object.

See Also

plotFunctions for plotting the top functional categories of a SQM object; plotBars for plotting a barplot with arbitrary data; mostAbundant for selecting the most abundant rows in a dataframe or matrix.

Examples

data(Hadza)
topPFAM = mostAbundant(Hadza$functions$PFAM$tpm)
topPFAM = topPFAM[rownames(topPFAM) != "Unclassified",] # Take out the Unclassified ORFs.
plotHeatmap(topPFAM, label_x = "Samples", label_y = "PFAMs", label_fill = "TPM")