plotHeat: Plotting a heatmap using pheatmap

In zktuong/kelvinny: Kelvinny The Incredible!

Description

Plotting a heatmap using pheatmap

Usage

plotHeat(
  d,
  color = "BluWhRd",
  scale = "row",
  genes = NULL,
  n = 50,
  alpha = 1,
  begin = 0,
  end = 1,
  option = "D",
  direction = 1,
  show_colnames = TRUE,
  show_rownames = TRUE,
  cluster_rows = TRUE,
  cluster_cols = TRUE,
  drop_levels = TRUE,
  fontsize = 9,
  legend = TRUE,
  border_color = NA,
  repel_degree = 0,
  ...
)

Arguments

color	Default has "BluWhRd", "RdWhBlu", "viridis" or a string of the colours you want. e.g. c("blue","yellow","orange").
scale	Default is "row". Other options include "column" or "none". see ?pheatmap.
genes	if provided, will highlight the vector provided in the rows
n	see ?viridis
alpha	see?viridis
begin	see ?viridis
end	see ?viridis
option	see ?viridis
direction	see ?viridis
show_colnames	TRUE/FALSE. see ?pheatmap.
show_rownames	TRUE/FALSE. see ?pheatmap.
cluster_rows	TRUE/FALSE. see ?pheatmap.
cluster_cols	TRUE/FALSE. see ?pheatmap.
drop_levels	TRUE/FALSE. see ?pheatmap.
fontsize	Default is 9. see ?pheatmap.
legend	TRUE/FALSE. see ?pheatmap.
border_color	see ?pheatmap.
repel_degree	amount of repel for flag. Only used if genes is specified
...	Passes on arguments to pheatmap.
data	A data frame containing values of interest. Genes in rows, samples across columns. if supplied as a matrix with rownames as genes and the 1st column is exprs values, it will still go through.

Value

A wrapper for pheatmap.

Examples

data(iris)
head(iris)
#   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
#1          5.1         3.5          1.4         0.2  setosa
#2          4.9         3.0          1.4         0.2  setosa
#3          4.7         3.2          1.3         0.2  setosa
#4          4.6         3.1          1.5         0.2  setosa
#5          5.0         3.6          1.4         0.2  setosa
#6          5.4         3.9          1.7         0.4  setosa
df <- iris[,c(1:4)]
plotHeat(df)

# using example from pheatmap
# Create test matrix
test = matrix(rnorm(200), 20, 10)
test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3
test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] + 2
test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)] + 4
colnames(test) = paste("Test", 1:10, sep = "")
rownames(test) = paste("Gene", 1:20, sep = "")
# Generate annotations for rows and columns
annotation_col = data.frame(
  CellType = factor(rep(c("CT1", "CT2"), 5)),
  Time = 1:5
)
rownames(annotation_col) = paste("Test", 1:10, sep = "")

annotation_row = data.frame(
  GeneClass = factor(rep(c("Path1", "Path2", "Path3"), c(10, 4, 6)))
)
rownames(annotation_row) = paste("Gene", 1:20, sep = "")
#plot!
plotHeat(test, annotation_col=annotation_col, annotation_row=annotation_row)

zktuong/kelvinny documentation built on Oct. 22, 2020, 1:27 p.m.