clusterSamplePheatmap: Compute and plot column correlation matrix. Normally used to...

In Tong-Chen/YSX: For Yishengxin Training

Description

Compute and plot column correlation matrix. Normally used to do sample corealtion of gene expression or OTU abundance matrix.

Usage

clusterSamplePheatmap(
  mat,
  method = "pearson",
  digits = 4,
  sampleAnno = NA,
  cellsize = NULL,
  cor_file = NULL,
  saveplot = NA,
  ...
)

Arguments

mat	A dataframe.
method	Type of correlation coefficient given to cor. Default "pearson".
digits	Number of decimial digits (given to round) to keep (default 4).
sampleAnno	Add sample attribute to plot. Accept a dataframe with rownames as "colnames(mat)".
cor_file	Save ordered correlation matrix to given file name.
saveplot	Save plot to given file "a.pdf", "b.png".
...	Additional parameters given to pheatmap like "width", "height", .etc.
Size	of cells. Default autodetect. This is used to get square plot.

Value

Nothing

Examples

df = generateAbundanceDF()
clusterSamplePheatmap(df)

Tong-Chen/YSX documentation built on Jan. 25, 2021, 2:49 a.m.