plotHeatmap: Function "plotHeatmap"

Description Usage Arguments Value

View source: R/plotHeatmap.R

Description

This function plots heat maps using given input matrix and group conditions

Usage

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plotHeatmap(geneExp, group, myPalette, legendName = "Gene expression",
  method = "ward.D2", distance = "spearman", rowCluster = TRUE,
  colCluster = TRUE, rowName = TRUE, colName = TRUE, s1 = 15,
  s2 = 8, s3 = 12, s4 = 6, s5 = 12, s6 = 100, s7 = 2, s8 = 4,
  s9 = 2, H, W, title = "Heatmap", Date)

Arguments

geneExp

a matrix, rows correspond to genes and columns correspond to samples if it is a gene expression matrix.

group

a data frame with each column a different column annotation which needs to be added to the heatmap, rownames correspond to sample ID.

myPalette

a named list with color palettes for each annotation, each element in the list should be a named vector.

legendName

name of the legend, default is "Gene expression".

method

a character type variable indicating the clustering method. Default is "ward.D2".

distance

a character type variable indicating the distance used for clustering. Default is "spearman".

rowCluster

a logical variable indicating whether to cluster the rows. Default is TRUE.

colCluster

a logical variable indicating whether to cluster the columns. Default is TRUE.

rowName

a logical variable indicating whether to show the row names. Default is TRUE.

colName

a logical variable indicating whether to show the column names. Default is TRUE.

s1

a numerical variable indicating the fontsize of legend title. Default is 15.

s2

a numerical variable indicating the fontsize of row names. Default is 8.

s3

a numerical variable indicating the fontsize of column names. Default is 12.

s4

a numerical variable indicating the height and width of grid in defined unit of column legend. Default is 6.

s5

a numerical variable indicating the width of the dendrogram for columns and rows. Default is 12.

s6

a numerical variable indicating the width of space for rowname and colname annotations. Default is 100.

s7

a numerical variable indicating the space between each top annotation. Default is 2.

s8

a numerical variable indicating the height of each column annotation. Default is 4.

s9

a numerical variable indicating the space between heatmap body and annotations. Default is 2.

H

a numerical variable indicating the height of saved figure. Default is 15.

W

a numerical variable indicating the width of save figure. Default is 15.

Date

a Date object obtained from Sys.Date

Value

a "HeatmapList" class object.


Coraline66/RNASeqAnalysis documentation built on Nov. 25, 2019, 8:03 a.m.