draw.2D.interactive: Visualize Sample Clustering Result in 2D Plot with...

In jyyulab/NetBID: Network-based Bayesian Inference of Drivers, version 2

Visualize Sample Clustering Result in 2D Plot with interactive mode

Description

draw.2D.interactive creats a 2D plot to visualize the sample clustering result with interactive mode realized by plotly.

Usage

draw.2D.interactive(
  X,
  Y,
  sample_label = NULL,
  color_label = NULL,
  shape_label = NULL,
  xlab = "PC1",
  ylab = "PC2",
  main = "",
  point_cex = 1,
  use_color = NULL,
  pre_define = NULL
)

Arguments

X	a vector of numerics, the x coordinates of points in the plot. If user would like to create a PCA biplot, this parameter should be the first component.
Y	a vector of numerics, the y coordinates of points in the plot. If user would like to create a PCA biplot, this parameter should be the second component.
sample_label	a vector of characters, name of samples to be displayed on the figure.
color_label	a vector of characters, labels used to define the point color.
shape_label	a vector of characters, labels used to define the point shape.
xlab	character, the label for x-axis. Default is "PC1".
ylab	character, the label for y-axis. Default is "PC2".
main	character, an overall title for the plot. Default is "".
point_cex	numeric, giving the amount by which the size of the data points should be magnified relative to the default. Default is 1.
use_color	a vector of color codes, colors to be assigned to each member of display label. Default is brewer.pal(9, 'Set1').
pre_define	a vector of characters, pre-defined color codes for a certain input (e.g. c("blue", "red") with names c("A", "B")). Default is NULL.

Value

Return the plotly class object for interactive visualization.

Examples

mat1 <- matrix(rnorm(2000,mean=0,sd=1),nrow=100,ncol=20)
rownames(mat1) <- paste0('Gene',1:nrow(mat1))
colnames(mat1) <- paste0('Sample',1:ncol(mat1))
pc <- stats::prcomp(t(mat1))$x
pred_label <- kmeans(pc,centers=4)$cluster ## this can use other cluster results
draw.2D.interactive(X=pc[,1],Y=pc[,2],
                    sample_label=rownames(pc),
                    color_label=pred_label,
                    pre_define = c('1'='blue','2'='red','3'='yellow','4'='green'))
draw.2D.interactive(X=pc[,1],Y=pc[,2],
                    sample_label=rownames(pc),
                    shape_label=pred_label)

jyyulab/NetBID documentation built on Dec. 23, 2024, 6:34 a.m.