plot-qntmap: Plot methods for 'qntmap' package

In atusy/qntmap: Enhance quantitative analysis of EPMA map

Description

S3 methods to plot object with original classes in qntmap package. See graphics::plot() for general use of plot. Mapping data (qm_xmap and qm_qntmap classes) are visualized by heat maps.

Usage

## S3 method for class 'qntmap'
plot(
  x,
  y = setdiff(names(x), c("x", "y"))[1L],
  zname = y,
  zlim = NULL,
  colors = c("magma", "viridis", "gray"),
  interactive = TRUE,
  unit = c("px", "um", "mm", "cm"),
  ...
)

## S3 method for class 'qm_xmap'
plot(
  x,
  y = setdiff(names(x), c("x", "y"))[1L],
  zname = y,
  zlim = NULL,
  colors = c("magma", "viridis", "gray"),
  interactive = TRUE,
  unit = c("px", "um", "mm", "cm"),
  ...
)

## S3 method for class 'qm_cluster'
plot(
  x,
  y = "cluster",
  zname = y,
  zlim = NULL,
  colors = c("magma", "viridis", "gray"),
  interactive = TRUE,
  unit = c("px", "um", "mm", "cm"),
  ...
)

Arguments

x	An object of class qntmap, qm_cluster, or qm_xmap, returned by quantify(), qntmap(), and read_xmap(), respectively.
zname, y	A string specifying a component of x to determine colors to fill the map. y is the alias of zname.
zlim	A range of z.
colors	A color scale "viridis" (default) or "gray" applicable when fill is continuous.
interactive	TRUE (default) produces plots with shiny WebUI, and FALSE produces plots with ggplot2::ggplot().
unit	Unit of x- and y-axis ("px", "um", "nm" or "cm").
...	Arguments passed to internal functions.

See Also

graphics::plot()

Examples

# qm_raster class object
d <- data.frame(expand.grid(x = 1:5, y = 1:5), fill = runif(5))
class(d) <- c("qm_raster", class(d))
plot(d, "fill", interactive = FALSE)

atusy/qntmap documentation built on April 11, 2021, 4:45 p.m.