plotFtCormat: Plot feature correlation matrix

In microresearcher/MicroVis: Microbiome Analysis and Visualization

Plot feature correlation matrix

Description

Plot feature correlation matrix

Usage

plotFtCormat(
  dataset1 = NULL,
  dataset2 = NULL,
  method = c("spearman", "pearson", "kendall"),
  factor = NULL,
  rank = NULL,
  sigsOnly = T,
  alpha = 0.05,
  adjustp = T,
  r_cutoff = 0,
  showlowrs = F,
  features1 = NULL,
  features2 = NULL,
  matchFts = F,
  theme = c("classic", "modern"),
  circles = F
)

Arguments

dataset1	MicroVis dataset. Defaults to the active dataset
dataset2	(Optional) MicroVis dataset with features to correlate with the dataset1
method	Correlation method. One of either "pearson", "spearman", or "kendall". Defaults to "spearman"
factor	Factor to group samples by
rank	Rank of features to use for calculation
sigsOnly	Select only significant correlations? Defaults to TRUE
alpha	Significance threshold. Defaults to 0.05
adjustp	Use the adjusted p-values? Defaults to TRUE
r_cutoff	Only select correlations with an absolute R-value above a certain threshold? This value must be between -1 and 1. Defaults to 0
showlowrs	(If r_cutoff is non-zero) Still shade correlations that are not above the correlation cutoff (r_cutoff)? Defaults to F
features1	(Optional) Specific features to consider from first dataset. If only one dataset is being used, then these features will be correlated with features of the same dataset
features2	(Optional) Specific features to consider from second dataset.
matchFts	Show the same features in the correlation matrices for all groups? This can be helpful when comparing correlations between groups. Defaults to FALSE
theme	Coloring theme. One of "classic" or "modern". Defaults to classic
circles	Use circles instead of squares to make the matrix? Defaults to FALSE

Value

List of the one or two datasets used for this plot

microresearcher/MicroVis documentation built on Feb. 8, 2024, 10:59 a.m.