In amitjavilaventura/seqViewR: Visualization of Omics And Sequencing Data In R

knitr::opts_chunk$set(echo = TRUE, warning = F, error = F, message = F,
                      fig.align = "center", fig.width = 6, fig.height = 4)

devtools::load_all("..")
library(dplyr)

chrom_sizes = "../testdata/mm10.chrom.sizes"
cyto_bands  = "../testdata/mm10.cytoBand.txt"
regions_list <- list("Regions1" = "../testdata/mm10.regions.tsv",
                     "Regions2" = "../testdata/mm10.regions2.tsv",
                     "Regions3" = "../testdata/mm10.regions3.tsv")


plotmics::chromRegions(chrom_sizes = chrom_sizes, regions_list = regions_list)

Last updated: r Sys.Date()

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Load plotmics

# load plotmics
library(plotmics)

Run chromRegions()

chromRegions() takes a file with the sizes of the chromosomes and draws a ggplot2-based bar plot. Then takes a list of regions in a BED-like format to draw them into each chromosome. The inputs chrom.sizes and regions can be supplied as a list of character with path to the file where the information is stored or a list of data frame.

Required input

The crhom_sizes input is:

chrom_sizes = "../testdata/mm10.chrom.sizes"
chrom_sizes %>% read.delim(header = F) %>% head()

The regions_list is a list of characters or dataframes. It can have as many elements as wanted and it has the following structure:

regions_list <- list("Regions1" = "../testdata/mm10.regions.tsv",
                     "Regions2" = "../testdata/mm10.regions2.tsv",
                     "Regions3" = "../testdata/mm10.regions3.tsv")
regions_list[[1]] %>% read.delim(header = F) %>% head()

Default run

The default run requires only the chrom_sizes and the regions arguments, either as a path to a file or a data frame.

chromRegions(chrom_sizes = "../testdata/mm10.chrom.sizes", regions_list = regions_list)

# Read the data
chrom_sizes = "../testdata/mm10.chrom.sizes"%>% read.delim(header = F)
regions = regions_list %>% purrr::map(~read.delim(.x, header = F))

chromRegions(chrom_sizes = chrom_sizes, regions_list = regions)

Chromosome order

chromRegions(chrom_sizes  = "../testdata/mm10.chrom.sizes", 
             regions_list = regions_list,
             chr_order    = c(1,3,4,2,5,6,7,9,8,19,11,10,12,13,15,14,16,17,18,"X","Y","M", "MT") )

Exclude chromosomes

Very often, the genome assemblies of a lot of species have chromosomes/scaffolds with strange names, which are not nice to plot. These can be excluded using the chr_exlude argument with a vector of regular expressions that match the chromosomes to exclude. By default chr_exclude removes the most usuall strange chromosomes, but if you want to remove more chromosomes or don't want to remove any, you can change the chr_exclude argument.

An example that excludes all the chromosomes that contain a dot in the name:

chromRegions(chrom_sizes  = "../testdata/mm10.chrom.sizes", 
             regions_list = regions_list,
             chr_exclude  = c("\\."))

Here you have an example that does not remove any chromosome.

chromRegions(chrom_sizes  = "../testdata/mm10.chrom.sizes", 
             regions_list = regions_list,
             chr_exclude  = c(" "))

Note that, since we are converting the chromosome names to an ordered factor with chr_order, the chromosome names that do not appear in chr_order will be groupped and plotted into a NA category.

Customization

Flip axes

chromRegions() allows flipping the axes by setting the coord_flip argument to TRUE.

chromRegions(chrom_sizes  = "../testdata/mm10.chrom.sizes", 
             regions_list = regions_list,
             coord_flip   = T)

Draw the points

By default, chromRegions() draws a line/rectangle and a point in the middle of each region. To avoid drawing the points, the argument draw_points can be set to FALSE.

chromRegions(chrom_sizes  = "../testdata/mm10.chrom.sizes", 
             regions_list = regions_list,
             draw_points  = F)

Color

By default, the regions are colored by region (i.e. each element in regions_list). This can be controlled with the colors argument, which accepts a character vector with valid color names and the same length as regions_list

chromRegions(chrom_sizes  = "../testdata/mm10.chrom.sizes", 
             regions_list = regions_list,
             colors       = c("Black", "Yellow", "Green"))

If you want to color by strand, just turn color_by to "strand".

chromRegions(chrom_sizes   = "../testdata/mm10.chrom.sizes", 
             regions_list  = regions_list,
             colors        = c("Darkgreen", "Darkred"),
             color_by      = "strand")

Now, imagine that we have regions that do not have a defined strand (e.g. most ChIP-seq peaks). In this case, the color_by is internally converted to "region" and the regions are colored by region set (i.e. elements in regions_list). Look at this example with only one region set whose strand values are converted to ".".

# Read and format regions file to have strand as "."
regions_no_strand <- list("Regions1" = read.delim("../testdata/mm10.regions.tsv", header = F) %>% dplyr::mutate(V6 = "."))

# Draw the plot
chromRegions(chrom_sizes   = "../testdata/mm10.chrom.sizes", 
             regions_list  = regions_no_strand,
             color_by      = "strand",
             colors        = c("Gold3", "Darkgreen"))

Titles

Title and subtitle can be supplied through the arguments title and subtitle, respectively. By default, they are set to NULL, but can accept a character of length 1.

chromRegions(chrom_sizes   = "../testdata/mm10.chrom.sizes", 
             regions_list  = regions_list,
             title         = "This is a title", 
             subtitle      = "This is a subtitle")

Also, the labels of the axes can be set or removed through the xlab and ylab arguments. By default, the X axis label is set to "Chromosome" and the Y axis is set to "", but they can be removed setting the corresponding arguments to NULL or changed to any value.

chromRegions(chrom_sizes   = "../testdata/mm10.chrom.sizes", 
             regions_list  = regions_list,
             xlab          = NULL,
             ylab          = "Position in the chromosome")

Finally, a caption can be included in the bottom-right corner by setting the caption argument. By default, caption is set to NULL and it can be set to TRUE or any character. If caption is set to a character, whatever is written will be placed in the bottom-right corner. Instead, if it is set to TRUE, what will be written will be the number of regions in the input region sets.

Here there is an example with any character:

chromRegions(chrom_sizes   = "../testdata/mm10.chrom.sizes", 
             regions_list  = regions_list,
             caption       = "This is a caption")

On the other hand, if caption is set to TRUE, the caption will show the number of regions in the input regions set (regions).

chromRegions(chrom_sizes   = "../testdata/mm10.chrom.sizes", 
             regions_list  = regions_list,
             caption       = TRUE)

Legend

The position of the legend is, by default, the bottom of the plot. This can be changed by changing the legend argument to one of "bottom", "right", "top", "left" or "none" (no legend). The legend argument is passed through ggpubr::theme_pubr().

chromRegions(chrom_sizes   = "../testdata/mm10.chrom.sizes", 
             regions_list  = regions_list,
             legend        = "right")

chromRegions(chrom_sizes   = "../testdata/mm10.chrom.sizes", 
             regions_list  = regions_list,
             legend        = "none")

Y axis

By default, the Y axis is not plotted, which means that the y_text_size is set to NULL. However, it can be plotted by setting the size_y_text argument to a number which will be used as size of the text in the Y axis.

chromRegions(chrom_sizes   = "../testdata/mm10.chrom.sizes", 
             regions_list  = regions_list, 
             y_text_size   =  10)

Further costumization

Since chromRegions() outputs a ggplot2-based bar plot, it can be further customized like any other ggplot2-based plot.

amitjavilaventura/seqViewR documentation built on Nov. 21, 2023, 10:12 a.m.