plotCorr: Correlation plot

In HimesGroup/qmtools: Quantitative Metabolomics Data Processing Tools

Correlation plot

Description

Visualizes correlations between samples or features with a SummarizedExperiment or matrix-like object where rows represent features and columns represent samples. A correlation matrix is visualized using a heatmap with dendrograms.

Usage

plotCorr(
  x,
  i,
  type = c("sample", "feature"),
  log2 = FALSE,
  use = c("everything", "all.obs", "complete.obs", "na.or.complete",
    "pairwise.complete.obs"),
  method = c("pearson", "kendall", "spearman"),
  dendrogram = TRUE,
  colors = (scales::viridis_pal())(256),
  label = FALSE,
  digits = 2,
  widths = c(0.8, 0.2),
  heights = c(0.2, 0.8),
  hide_colorbar = FALSE,
  showticklabels = c(TRUE, TRUE),
  row_dend_left = FALSE,
  k_row = 1,
  k_col = 1,
  ...
)

Arguments

x	A matrix-like object or SummarizedExperiment object.
i	A string or integer value specifying which assay values to use when x is a SummarizedExperiment object.
type	A string specifying whether a correlation matrix is computed based on samples or features.
log2	A logical specifying whether feature intensities needs to be log2-transformed before calculating a correlation matrix.
use	A string specifying which method to compute correlations in the presence of missing values. Refer to ?cor for details.
method	A string specifying which correlation coefficient is to be computed. See ?cor for details.
dendrogram	A logical specifying whether dendogram is computed and reordering is performed.
colors	A vector of colors for the heatmap.
label	A logical specifying whether cell values are shown.
digits	A numeric value specifying the desired number of digits when label = TRUE.
widths	A numeric vectors specifying relative widths of heatmap and dendrogram.
heights	A numeric vectors specifying relative heights of heatmap and dendrogram.
hide_colorbar	A logical specifying whether the color bar (legend) is hidden.
showticklabels	A logical vector of length 2 (x-axis, y-axis) specifying whether the ticks are removed from the sides of the plot.
row_dend_left	A logical controlling whether the row dendrogram is placed on the left on the plot.
k_row	A numeric value specifying the desired number of groups by which to color the dendrogram's branches in the rows. If NA, then dendextend::find_k is used to deduce the optimal number of clusters.
k_col	A numeric value specifying the desired number of groups by which to color the dendrogram's branches in the columns. If NA, then dendextend::find_k is used to deduce the optimal number of clusters.
...	Additional arguments passed to heatmaply::heatmaply.

Value

A patchwork object of aligned ggplots.

References

Tal Galili, Alan O'Callaghan, Jonathan Sidi, Carson Sievert; heatmaply: an R package for creating interactive cluster heatmaps for online publishing, Bioinformatics, btx657, https://doi.org/10.1093/bioinformatics/btx657

Examples

data(faahko_se)

## Sample group
g <- colData(faahko_se)$sample_group

## SummarizedExperiment object
plotCorr(faahko_se, i = "knn_vsn", method = "spearman", k_col = 4)

## Matrix
m <- assay(faahko_se, "knn_vsn")
plotCorr(m[1:50, ], type = "feature", method = "spearman")

HimesGroup/qmtools documentation built on April 16, 2023, 8 p.m.