tests_not_run/test_chromatin_states_transition.R

In jokergoo/epik: Integrative Analysis and Visualization of Epigenomic Sequencing Data

source("/home/guz/project/development/epik/tests/test_head.R")
source("/home/guz/project/development/epik/R/chromatin_states_transitions.R")
library(circlize)
library(ComplexHeatmap)
library(EnrichedHeatmap)
library(matrixStats)
library(Rcpp)
sourceCpp("/home/guz/project/development/epik/src/rowWhichMax.cpp")

states_list = get_chromHMM_list(sample_id, c("chr21", "chr22"))

methdiff = 0

gr_list_1 = states_list[subgroup == "group1"]
gr_list_2 = states_list[subgroup == "group2"]

mat = make_transition_matrix_from_chromHMM(gr_list_1, gr_list_2, methylation_diff = methdiff)
mat

sn = state_names(mat)
od = order(as.numeric(gsub("^(\\d+)_.*$", "\\1", sn)))
mat = mat[od, od]
state_names(mat) = gsub("\\d+_", "", state_names(mat))

## color setting and make the plot
state_col = c("TssA" = "#E41A1C",
	          "TssAFlnk" = "#E41A1C",
	          "TxFlnk" = "#E41A1C",
	          "Tx" = "#E41A1C",
	          "TxWk" = "#E41A1C",
	          "EnhG" = "#E41A1C",
	          "Enh" = "#E41A1C",
	          "ZNF/Rpts" = "#E41A1C",
	          "Het" = "#377EB8",
	          "TssBiv" = "#377EB8",
	          "BivFlnk" = "#377EB8",
	          "EnhBiv" = "#377EB8",
	          "ReprPC" = "#377EB8",
	          "ReprPCWk" = "#377EB8",
	          "Quies" = "black")

chromatin_states_transition_chord_diagram(mat, state_col = state_col, group_names = c("g1", "g2"),
	legend_position = c("bottomleft", "bottomright"))


methylation_hooks(RESET = TRUE)
mat = make_transition_matrix_from_chromHMM(gr_list_1, gr_list_2)
mat

sn = state_names(mat)
od = order(as.numeric(gsub("^(\\d+)_.*$", "\\1", sn)))
mat = mat[od, od]
state_names(mat) = gsub("\\d+_", "", state_names(mat))
chromatin_states_transition_chord_diagram(mat, state_col = state_col, group_names = c("g1", "g2"),
	legend_position = c("bottomleft", "bottomright"))