plot_kmeans_pheatmap: plot kmeans pheatmap

In jiang-junyao/IReNA: IReNA

plot kmeans pheatmap

Description

Display the result of clustering based on pheatmap, the input data.frame should contain KmeansGroup column.

Usage

plot_kmeans_pheatmap(
  Kmeans_result,
  start_column = 3,
  Gene1 = NULL,
  NumRowBlank1 = 20,
  show_colnames = FALSE,
  clustering_distance_rows = "correlation",
  ModuleColor1 = NULL,
  ModuleScale1 = 20,
  cluster_cols = FALSE,
  fontsize = 10,
  legend1 = TRUE,
  border_color = "white",
  ByPanel = FALSE,
  Color1 = NULL,
  Show.Module = TRUE,
  Range1 = c(-3, 3),
  ColumnGroup1 = NULL
)

Arguments

Kmeans_result	expression profile which should contain column "KmeansGroup"
start_column	numeric, indicating the start column of expression value, defalut is 3
Gene1	custom labels for rows that are used instead of rownames
NumRowBlank1	the blank between each group
show_colnames	logic, indicating whether show column names, default is FALSE
clustering_distance_rows	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
ModuleColor1	each color for each module
ModuleScale1	change the relative proportion of module bar and expression heatmap
cluster_cols	boolean values determining if columns should be clustered or hclust object.
fontsize	font size
legend1	logic, indicating whether show the legend, default is TRUE
border_color	color of cell borders on heatmap, use NA if no border should be drawn.
ByPanel	logic, if TRUE, reorder columns of heatmap according to the parameter ColumnGroup1, default is FALSE
Color1	colors used in heat map
Show.Module	logic, indicating whether show the module, defalut is TURE
Range1	numeric, indicating the range of expression values which will affect the range of heat map, defalut is c(-3, 3)
ColumnGroup1	vector, if it is not NULL, this function wil sepate columns according to varible ColumnGroup1, default is NULL

Value

Kmeans clustering figure

Examples

col1 <- c('#67C1E3','#EF9951','#00BFC4','#AEC7E8','#C067A9','#E56145','#2F4F4F')
load(system.file("extdata", "test_clustering.rda", package = "IReNA"))
plot_kmeans_pheatmap(test_clustering, ModuleColor1 = col1,Range1=c(-3,3),NumRowBlank1=1,ModuleScale1 = 20)

jiang-junyao/IReNA documentation built on Nov. 15, 2024, 1:51 a.m.