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

Description Usage Arguments Value

View source: R/heatmap.R

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

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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 July 13, 2017, 6:33 a.m.