corHeatmap: Correlation heatmap of sections

In tomoda: Tomo-seq data analysis

Description

Heatmap pf correlation coefficients between any two sections in a SummarizedExperiment object.

Usage

corHeatmap(object, matrix = "scaled", max.cor = 0.5, cor.method = "pearson")

Arguments

object	A SummarizedExperiment object.
matrix	Character, must be one of "count", "normalized", or "scaled".
max.cor	Numeric, correlation coefficients bigger than max.cor are set to max.cor. It is used to clearly show small correlation coefficients.
cor.method	Character, the method to calculate correlation coefficients. must be one of "pearson", "kendall", or "spearman".

Value

A ggplot object.

Examples

data(zh.data)
zh <- createTomo(zh.data)
corHeatmap(zh)

# Use Spearman correlation coefficients.
corHeatmap(zh, cor.method='spearman')

# Set max correlation coefficients to 0.3.
corHeatmap(zh, max.cor=0.3)

tomoda documentation built on Nov. 8, 2020, 8:10 p.m.