plotPeakImage: plotPeakImage.

Description Usage Arguments

View source: R/plotPeakMatrix.R

Description

plot the ion image map of a given mass or column of a rMSIproc peak matrix object. If the peak matrix contains data from various datasets the images will be layout horizontally or vertically. At leas mz or column must be specified.

Usage

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plotPeakImage(
  peakMatrix,
  mz = NULL,
  column = NULL,
  matrix = "intensity",
  normalization = NULL,
  nrow = 2,
  ncol = 2,
  byrow = T,
  margin = 20,
  img_names = peakMatrix$names,
  labels = img_names,
  rotations = rep(0, length(img_names)),
  mirror_x = rep(F, length(img_names)),
  mirror_y = rep(F, length(img_names)),
  pixel_size_um = 100,
  light = 8
)

Arguments

peakMatrix

the peak matrix in an rMSIproc object.

mz

the peak mass to plot, the nearest peak mass will be ploted.

column

the column of the peak matrix to plot.

matrix

the name of the peak matrix to plot.

normalization

the name of normalization to use.

nrow

number of rows of the plotted matrix layout (only used if byrow == F)

ncol

number of cols of the plotted matrix layout (only used if byrow == T)

byrow

a bool specifing if images must be arranged in rows.

margin

the separation between plotted images.

img_names

a character vector with img names in the desierd plotting order.

labels

an alternative character vector with the labels to be displayed for each image.

rotations

a vector with the rotation of each images specified in degrees.

mirror_x

a bool vector specifing if each image must be flipped or not in X direction prior to rotation.

mirror_y

a bool vector specifing if each image must be flipped or not in Y direction prior to rotation.

pixel_size_um

the pixel resolution in um.

light

the lighting of the plotted image.


prafols/rMSIproc documentation built on Dec. 12, 2021, 7:31 p.m.