Plot Image Maps

Plotting function for objects of the foldchange_matrix, outlier_map, or missingness_map classes. Produces a heatmap-style image using ggplot2 syntax, for objects produced by one of calcFoldchangeMatrix(), calcOutlierMap(), or calcMissingnessMap().

Usage

# S3 method for Map
plot(
  x,
  color.scheme = NULL,
  legend.ticks = 7,
  gridlines = NULL,
  gridlinecol = "red",
  gridlinelwd = 0.5,
  gridlinelty = 2,
  main = NULL,
  y.lab = NULL,
  x.lab = NULL,
  type = c("foldchange", "outlier", "missingness"),
  flags = NULL,
  legend.width = 1,
  legend.height = 2,
  filename = NULL,
  plot.width = 14,
  plot.height = 8,
  plot.scale = 1,
  ...
)

Arguments

x

An object of class:

• foldchange_matrix

• outlier_map

• missingness_map

color.scheme

Which color scheme to use. Typical choices include:

• gplots::redgreen()

• gplots::bluered()

• grDevices::heat.colors()

• grDevices::terrain.colors()

• grDevices::topo.colors()

• RColorBrewer::brewer.pal()

• viridis::viridis()

• viridis::magma()

legend.ticks

How many ticks to place on the color legend.

gridlines

Numeric vector or logical. Indicates where to draw the horizontal grid lines that can be used to separate samples (rows). This should be a vector of the cumulative sum of the horizontal lines to be drawn, typically something like cumsum(table(data$Sex)). Alternatively, TRUE can be passed whereby the lines are determined by the "class.tab" element of x$class.tab (if possible).

gridlinecol

Color of the gridlines.

gridlinelwd

Width of the gridlines.

gridlinelty

Line type of the gridlines.

main

Character. Main title for the plot. See ggtitle() for ggplot2 style graphics.

y.lab

Character. Optional string for the y-axis. Otherwise one is automatically generated (default).

x.lab

Character. Optional string for the x-axis. Otherwise one is automatically generated (default).

type

Character. Currently one of: "foldchange", "outlier", or "missingness". This argument is determined by object class and typically should not have to be passed by the user if called via the intended S3 plot method.

flags

Numeric in [0, 1]. For an "outlier_map", the proportion of the analytes (columns) for a given sample that must be outliers for a flag to be placed at the right-axis, thus flagging that sample. For "missingness_map" class, the percent of "missingness" (NAs) of the clinical meta data. If NULL (default), 0.05 (5%) is selected.

legend.width

Width for the color legend.

legend.height

Height for the color legend.

filename

Optional. If provided, the plot will be written to a file. The file name must also include the desired file type extension; this will be used to determine the file type, e.g. a file named foo.png will be saved as a PNG. See ggsave() for a full list of file type (device) options.

plot.width

If "filename != NULL", the width of the plot image file.

plot.height

If "filename != NULL", the height of the plot image file.

plot.scale

If "filename != NULL", the scale of the plot image file.

...

Arguments required by the plot() generic. Currently unused.

Value

Plot an image of the passed matrix.

See also

ggplot(), geom_raster()

Other Calc Map: calcFoldchangeMatrix(), calcMissingnessMap(), calcOutlierMap(), getFlaggedIds()

Author

Stu Field, Amanda Hiser

Examples

data <- SomaDataIO::example_data

# Fold-change
FC <- calcFoldchangeMatrix(data)
plot(FC)


# Outlier
OM <- calcOutlierMap(data)
plot(OM, flags = 0.05)


# Clin Data Missingness
meta <- SomaDataIO::getMeta(data)
MM   <- calcMissingnessMap(data[, meta])
plot(MM, flags = 0.05)