transition2hm()

Adrià Mitjavila Ventura

13 May, 2021

Source: vignettes/02-transition2hm.Rmd

Default transitions from ChromHMM

knitr::include_graphics("../demodata/transitions_8.png")

Run chromHMMviewR

Install and load

# install devtools if not installed
if(!require(devtools)){ install.packages("devtools") }

# install chromHMMviewR if not installed
if(!require(chromHMMviewR)){ devtools::install_github("amitjavilaventura/chromHMMviewR") }
# load chromHMMviewR
library(chromHMMviewR)

Read and explore data

# read emissions file from the demodata
transitions <- read.delim("../demodata/transitions_8.txt")

# head
head(transitions)
##   state..from.to...Emission.order.           X1           X2           X3
## 1                                1 0.6237799631 5.969936e-02 1.444232e-01
## 2                                2 0.0361653826 6.125980e-01 1.588527e-01
## 3                                3 0.0667223477 1.305861e-01 7.980450e-01
## 4                                4 0.0003346948 5.910215e-05 5.557259e-05
## 5                                5 0.0000000000 3.388524e-02 1.394200e-03
## 6                                6 0.0098823093 1.613592e-02 3.031194e-05
##            X4          X5           X6           X7           X8
## 1 0.014670208 0.000000000 0.1119489415 0.0374990405 0.0079792596
## 2 0.001697886 0.083028122 0.1073994222 0.0002585049 0.0000000000
## 3 0.001039399 0.002886479 0.0002521457 0.0004685915 0.0000000000
## 4 0.963817428 0.001988460 0.0289758412 0.0039176834 0.0008512181
## 5 0.022452888 0.822001613 0.1188773437 0.0013887126 0.0000000000
## 6 0.120611407 0.044797589 0.7424068235 0.0585232267 0.0076124152

Call transition2hm()

Minimum

# set the states with numbers
# states should be named later depending on the results
states <- paste("S", 1:8, sep = "")
# call transition2hm()
transition2hm(data = transitions, states = states)
## Loading required package: dplyr
## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
## Loading required package: magrittr
## Loading required package: reshape2
## Loading required package: ggplot2
## Loading required package: ggpubr
## Using State as id variables

From a file

# call transition2hm()
transition2hm(data = "../demodata/transitions_8.txt", states = states)
## Using State as id variables

Customize the output

# change title, subtitle, xlab and ylab
transition2hm(data = transitions, states = states, 
              title = "This is a title", 
              subtitle = "This is a subtitle", 
              xlab = "This is the x-axis title",
              ylab = "This is the y-axis title")
## Using State as id variables

# change color of the heatmap: color = "gray30"
transition2hm(data = transitions, states = states, color = "gray30")
## Using State as id variables

# change the size of the likelihood labels (default: lh_size = 2)
transition2hm(data = transitions, states = states, lh_size = 4)
## Using State as id variables

# without likelihood labels: show_lh = F
transition2hm(data = transitions, states = states, show_lh = F)
## Using State as id variables