poplin_corplot: Correlation plot

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

Description

Visualize correlations between samples or features. All values in a correlation matrix are visualized by rectangles.

Usage

## Default S3 method:
poplin_corplot(
  x,
  unit = c("sample", "feature"),
  use = c("everything", "all.obs", "complete.obs", "na.or.complete",
    "pairwise.complete.obs"),
  method = c("pearson", "kendall", "spearman"),
  widths = NULL,
  heights = NULL,
  colors = viridis::viridis(n = 256, alpha = 1, begin = 0, end = 1, option = "viridis"),
  label = FALSE,
  digits = 2,
  grid_gap = 0,
  hide_colorbar = FALSE,
  showticklabels = c(TRUE, TRUE),
  row_dend_left = FALSE,
  ...
)

## S3 method for class 'poplin'
poplin_corplot(
  x,
  xin,
  unit = c("sample", "feature"),
  use = c("everything", "all.obs", "complete.obs", "na.or.complete",
    "pairwise.complete.obs"),
  method = c("pearson", "kendall", "spearman"),
  widths = NULL,
  heights = NULL,
  colors = viridis::viridis(n = 256, alpha = 1, begin = 0, end = 1, option = "viridis"),
  label = FALSE,
  digits = 2,
  grid_gap = 0,
  hide_colorbar = FALSE,
  showticklabels = c(TRUE, TRUE),
  row_dend_left = FALSE,
  ...
)

Arguments

x	A matrix or poplin object.
unit	Character specifying whether a correlation matrix is computed based on samples or features.
use	The method to compute correlations in the presence of missing values. Refer to ?cor for details.
method	character specifying which correlation coefficient is to be computed. Refer to ?cor for details.
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_corplot(faahko_poplin, xin = "knn_cyclic")

## matrix
m <- poplin_data(faahko_poplin, "knn_cyclic")
poplin_corplot(m, label = TRUE)

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