heatmap_plot: Creates a heatmap plot fork by raivokolde/pheatmap wrap and...

In jamebluntcc/myRtools: a collection of many useful graphic tools

Description

The function also allows to aggregate the rows using kmeans clustering. This is advisable if number of rows is so big that R cannot handle their hierarchical

Usage

heatmap_plot(data, Scale = "column", showRowNames = F,
  showColNames = TRUE, borderColor = "grey", clusterRows = TRUE,
  clusterCols = TRUE, clusterDistanceRows = "euclidean",
  clusterDistanceCols = "euclidean", clusterMethod = "complete",
  treeHeightRow = 0, clusterLegend = TRUE, Main = NA, fontSize = 10,
  fontSizeRow = fontSize, fontSizeCol = fontSize, clusterGroup = NA,
  Color = colorRampPalette(rev(RColorBrewer::brewer.pal(n = 7, name =
  "RdYlGn")))(100), saveType = c("both", "pdf", "png"), fileName = NULL,
  filePath = "", width = 8, height = 6)

Arguments

data	numeric matrix of the values to be plotted.
Scale	character indicating if the values should be centered and scaled in either the row direction or the column direction, or none. Corresponding values are "row", "column" and "none" default is "column"
borderColor	color of cell borders on heatmap, use grey if no border should be drawn.
clusterRows	boolean values determining if rows should be clustered or hclust object,
clusterCols	boolean values determining if columns should be clustered or hclust object.
Main	the title of the plot
fontSize	base fontsize for the plot
fontSizeRow	fontsize for rownames (Default: fontsize)
fontSizeCol	fontsize for colnames (Default: fontsize)
clusterGroup	a list of character to divide your group,default is NA.
fileName	file name. Filetype is decided by the extension in the path. Currently following formats are supported: png, pdf, tiff, bmp, jpeg. Even if the plot does not fit into the plotting window, the file size is calculated so that the plot would fit there, unless specified otherwise.
filePath	file path where to save the picture.
color	vector of colors used in heatmap.
clusteringDistanceRows	distance measure used in clustering rows. Possible values are "correlation" for Pearson correlation and all the distances supported by dist, such as "euclidean", etc. If the value is none of the above it is assumed that a distance matrix is provided.
clusteringDistanceCols	distance measure used in clustering columns. Possible values the same as for clustering_distance_rows.
clusteringMethod	clustering method used. Accepts the same values as hclust.
treeHeightCol	the height of a tree for columns, if these are clustered. Default value 50 points.
legend	logical to determine if legend should be drawn or not.
Width	manual option for determining the output file width in inches.
Height	manual option for determining the output file height in inches.

Value

A heatmap plot file of pdf or png.

jamebluntcc/myRtools documentation built on May 17, 2019, 2:44 p.m.