neighbor2hm()

Adrià Mitjavila Ventura

13 May, 2021

Source: vignettes/04-neighbor2hm.Rmd

Default overlap from ChromHMM

knitr::include_graphics("../demodata/conditionX_8_RefSeqTSS_neighborhood.png")

Run chromHMMviewR::neighbor2hm()

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 the data

# read neighborhood file from the demodata
tss_neighbor <- read.delim("../demodata/conditionX_8_RefSeqTSS_neighborhood.txt")

# head
head(tss_neighbor)
##   State..Emission.order.  X.2000   X.1800   X.1600   X.1400   X.1200   X.1000
## 1                      1 4.68205  5.66775  7.02308  9.24089 10.93848 14.62115
## 2                      2 9.62928 12.94596 17.09522 21.17623 25.56435 28.20540
## 3                      3 4.74970  5.46034  7.07016  9.91997 13.65447 19.92697
## 4                      4 2.52862  2.37108  2.17270  1.94729  1.70008  1.41940
## 5                      5 3.97564  4.32704  4.48207  4.63365  4.66810  4.61642
## 6                      6 4.58853  4.72869  4.85287  4.87008  5.03730  5.18853
##      X.800    X.600    X.400    X.200       X0     X200     X400     X600
## 1 18.13953 26.27152 38.82544 60.14110 66.75348 47.91574 37.33321 31.21369
## 2 31.13991 33.60353 32.52527 20.78724  9.67705 10.16159 12.81630 18.51470
## 3 28.13560 36.40225 45.04597 54.18279 66.57550 77.11185 78.38811 72.64496
## 4  1.14700  0.94985  0.86079  0.82885  0.82916  0.84083  0.87062  0.91914
## 5  4.51996  4.02042  2.93177  1.99471  1.49862  1.40560  1.35048  1.27124
## 6  4.92049  4.05000  2.90410  2.20697  1.75205  1.53811  1.51844  1.61557
##       X800    X1000    X1200    X1400    X1600    X1800    X2000
## 1 28.61254 26.87389 23.50610 18.35858 12.75928  8.13199  5.22966
## 2 28.56710 41.10359 48.70602 46.35158 37.32285 25.91922 16.84954
## 3 58.97599 39.94095 23.55269 13.48769  8.00559  5.03975  3.65473
## 4  0.96797  1.02938  1.10432  1.22132  1.38899  1.60519  1.88465
## 5  1.34359  1.57441  1.99471  2.70784  3.47610  4.24435  4.82313
## 6  1.87500  2.32992  3.25082  4.61557  6.07992  7.18525  7.29836

Call neighbor2hm()

Minimum run

# set the states with numbers
# states should be named later depending on the results
states <- paste("S", 1:8, sep = "")
# call neighbor2hm()
neighbor2hm(data = tss_neighbor, 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: ggplot2
## Loading required package: stringr
## Loading required package: magrittr
## Loading required package: reshape2
## Loading required package: ggpubr
## Loading required package: purrr
## 
## Attaching package: 'purrr'
## The following object is masked from 'package:magrittr':
## 
##     set_names
## Using State as id variables

From a file

# call neighbor2hm()
neighbor2hm(data = "../demodata/conditionX_8_RefSeqTSS_neighborhood.txt", states = states)
## Using State as id variables

Customize the output

# change title, subtitle and xlab
neighbor2hm(data = tss_neighbor, states = states, 
            title = "This is a title", subtitle = "This is a subtitle", 
            xlab = "This is the x-axis title")
## Using State as id variables

# change color of the heatmap: color = "gray30"
neighbor2hm(data = tss_neighbor, states = states, color = "gray30")
## Using State as id variables

# show the enrichment values in each cell
neighbor2hm(data = tss_neighbor, states = states, show_score = T) 
## Using State as id variables

# change the size of the erichment values (default: score_size = 2)
neighbor2hm(data = tss_neighbor, states = states, show_score = T, score_size = 1)
## Using State as id variables