WOTPLY: WOTPLY

In WOTPLY: Plot Connectivity Between Cells from Different Time Points

WOTPLY

Description

A ggnet2 plot is generated showing the connections between selected_stages from the latest time point and the clusters from previous time points . The number of columns is equal to the numbers of time points. In each column, the cluster of the corresponding time point is shown as network node. The weight of the links between clusters at time points t and t+1 reflect the weight of the transition probabilities from list_transition_matrices.

Usage

WOTPLY(
  list_transition_matrices,
  selected_stages,
  cluster_label,
  legend_time,
  customize_color,
  top_link = NULL
)

Arguments

list_transition_matrices	List of transition matrices. Each matrix contains the transition probabilitiesfrom the clusters at time t (on the columns) towards the clusters at time t+1 (on the rows). The matrices can be obtain from function get_transition_matrix
selected_stages	Vector with the name of the clusters related to the latest time point for which we want to know the connection to clusters at previous time points.
cluster_label	Vector with the cluster information for all the cells from all time points.
legend_time	Vector with time information with length equal to the number of time points.
customize_color	Character vector with the name of the colour for each cluster (node) in each time point.
top_link	Integer.Maximum number of links to select between clusters at time t and clusters at time t+1. Links are sorted according to the weight and then only the top_link are kept. If NULL (default), all the links are kept.

Value

A ggnet2 plot

Author(s)

Gabriele Lubatti [e-mail]

See Also

https://CRAN.R-project.org/package=GGally

Examples

transition_1 <- matrix(1,ncol = 2,nrow = 2)
colnames(transition_1) <- c("Stage1", "Stage2")
row.names(transition_1) <- c("Stage1", "Stage2")
l_t <- list((transition_1))
selected_stages <- c("Stage1")
cluster_label <- c("Stage1", "Stage2")
legend_time <- c("Day1", "Day2")
customize_color <- c("#F8766D", "#00BFC4")
WOTPLY(l_t, selected_stages, cluster_label, legend_time, customize_color)

WOTPLY documentation built on Sept. 12, 2022, 9:05 a.m.