Download Package `TCGAbiolinks`

TCGAvisualize_Heatmap
row.metadata
Metadata for the rows genes (expression) or probes (methylation)
col.colors
A list of names colors
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row.colors
A list of named colors
show_column_names
Show column names names? Dafault: FALSE
show_row_names Show row names? Dafault: FALSE
cluster_rows
Cluster rows ? Dafault: FALSE
cluster_columns
Cluster columns ? Dafault: FALSE
sortCol
Name of the column to be used to sort the columns
extrems
Extrems of colors (vector of 3 values)
rownames.size
Rownames size
title
Title of the plot
color.levels
A vector with the colors (low level, middle level, high level)
values.label
Text of the levels in the heatmap
filename
Filename to save the heatmap. Default: heatmap.png
width
figure width
height
figure height
type
Select the colors of the heatmap values. Possible values are "expression" (default), "methylation"
Use z-score to make the heatmap? If we want to show differences between
genes, it is good to make Z-score by samples (force each sample to have zero
mean and standard deviation=1). If we want to show differences between samples, it is good to make Z-score by genes (force each gene to have zero mean
and standard deviation=1). Possibilities: "row", "col". Default "none"
heatmap.legend.color.bar
Heatmap legends values type. Options: "continuous", "disctrete
scale
Value
Heatmap plotted in the device
Examples
row.mdat <- matrix(c("FALSE","FALSE",
"TRUE","TRUE",
"FALSE","FALSE",
"TRUE","FALSE",
"FALSE","TRUE"
),
nrow = 5, ncol = 2, byrow = TRUE,
dimnames = list(
c("probe1", "probe2","probe3","probe4","probe5"),
c("duplicated", "Enhancer region")))
dat <- matrix(c(0.3,0.2,0.3,1,1,0.1,1,1,0, 0.8,1,0.7,0.7,0.3,1),
nrow = 5, ncol = 3, byrow = TRUE,
dimnames = list(
c("probe1", "probe2","probe3","probe4","probe5"),
c("TCGA-DU-6410",