poplin_naplot: Missing value plot

In jaehyunjoo/poplin: LC/MS Metabolomics Data Processing Utilities

Description

Visualize data for exploring missing value (NA) patterns. All values in a data matrix are recoded (1: missing; 0: non-missing) and visualized by rectangles.

Usage

## Default S3 method:
poplin_naplot(
  x,
  widths = NULL,
  heights = NULL,
  colors = viridis::viridis(2),
  label = FALSE,
  digits = 2,
  grid_gap = 1,
  hide_colorbar = TRUE,
  showticklabels = c(TRUE, FALSE),
  row_dend_left = FALSE,
  ...
)

## S3 method for class 'poplin'
poplin_naplot(
  x,
  xin,
  widths = NULL,
  heights = NULL,
  colors = viridis::viridis(2),
  label = FALSE,
  digits = 2,
  grid_gap = 1,
  hide_colorbar = TRUE,
  showticklabels = c(TRUE, FALSE),
  row_dend_left = FALSE,
  ...
)

Arguments

x	A matrix or poplin object.
widths	Relative widths of heatmap and dendrogram.
heights	Relative heights of heatmap and dendrogram.
colors	A vector of colors for heatmap.
label	Logical controlling whether cell values are shown.
digits	The desired number of digits when label = TRUE.
grid_gap	Numeric specifying the gap between cells.
hide_colorbar	Logical controlling whether the color bar (legend) is hidden.
showticklabels	A logical vector of length 2 (x-axis, y-axis). If FALSE, the ticks are removed from the sides of the plot.
row_dend_left	Logical controlling whether the row dendrogram is placed on the left on the plot.
...	Additional arguments passed to heatmaply (heatmaply package).
xin	Character specifying the name of data to retrieve from x when x is a poplin object.

Value

A gtable of aligned plots

Examples

data(faahko_poplin)

## poplin object
poplin_naplot(faahko_poplin, xin = "raw")

## matrix
m <- poplin_raw(faahko_poplin, "raw")
poplin_naplot(m)

jaehyunjoo/poplin documentation built on Jan. 8, 2022, 1:13 a.m.