plotHeatmap_I: Function "plotHeatmap_I"

Description Usage Arguments Value

View source: R/plotHeatmap_I.R

Description

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

Usage

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plotHeatmap_I(condition = c("mutant", "wildtype"), geneES, group,
  palette, legendName = "Gene expression", distance = "spearman",
  method = "ward.D2", rowCluster = TRUE, colCluster = TRUE,
  rowName = TRUE, colName = TRUE, title, s1 = 15, s2 = 4,
  s3 = 11, s4 = 6, s5 = 12, s6 = 100, s7 = 2, s8 = 4, s9 = 2,
  H = 11, W = 28, Date)

Arguments

condition

a character type vector of the grouping annotation indicated in the pData(geneES).

geneES

an ExpressionSet object containing the input matrix and annotation data(one column of SampleID and the other of Group)

group

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

palette

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".

distance

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

method

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

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.

title

a character variable representing the title of the heatmap.

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.