In andronekomimi/SNPVizualTools: Suite of R tools for custom SNP vizualisation

SNPVizualTools Basics

Loading SNPVizualTools package and dependencies

suppressMessages(library(SNPVizualTools))

How to generate a basic vizualisations

First define the chromosome you want to study (current_chr) and get the available data (my.data) for this chromosome:

current_chr <- "chr12"
my.data <- loadChrData()

The define the area to vizualise:

current_range <- setStudyRange(27950000, 28735000)

The loaded data will be screened and the found interactions will transform into Genomic Ranges (my.ranges):

my.ranges <- getDataOverview()

The my.ranges variable is a list containing three elements: arch, circos and lncrna. Each element is designed for a type of visual representation:

• arch will be used with the function drawArchs

• circos will be used with the function drawCircos

• lncrna will be used with the function drawLncrnas

Draw Archs

You can draw the HiC and ChIA-PET arches with functions drawArchs to generate ggplot arches and tracks to print them. By default, this function uses my.ranges data.

arches_track <- drawArchs()
tracks(arches_track) + xlim(current_range)

If you want to highlight some regions, you can provide a list of highlight regions. A highlight region will be generated throught the setHighLight function. This function needs a start and a stop to define the region to highlight and a method defining the way to highlight this specific zone (by increasing its alpha or changing its color):

specific_range1 <- setHighLight(28111017,28127138,"alpha")
specific_range2 <- setHighLight(28284682,28287682,"alpha")
specific_range3 <- setHighLight(28284682,28287682,"color")

arches_track <- drawArchs(highlight_range_list = list(specific_range1,specific_range2, specific_range3))
tracks(arches_track) + xlim(current_range)

By default, all the replicates of an experiment are processed individually. After generated the my.ranges variable, you can manually merged some lines :

k562_chiapet <- mergeRanges(c(my.ranges$arch$sgp_k562_lane13, my.ranges$arch$sgp_k562_lane24), label = "K562 ChiA-PET SGP")

You can vizualise the resulting figure like that :

specific_range1 <- setHighLight(28111017,28127138,"alpha")

custom_track <- drawArchs(ranges_list = k562_chiapet, highlight_range_list = list(specific_range1))
tracks(custom_track) + xlim(current_range)

To re-organize (select, order and/or merge) several the ranges you can use the powerful function organizeRanges. You have to provide a vector with the index of the tracks if you have already generated a first figure with all the informative tracks (track_index) OR a vector with the index of the range how they appear in my.range (range_index) and a vector with the labels of tracks if you want to change them. The following syntax indicate you to merge two or more tracks : 1;4.

Here is an example :

index = c("1;2;4","3;5","9","7")
labels =  c("Chiapet 1", "Chiapet 2", "HiC 2", NA)
custom_ranges <- organizeRanges(track_index = index, labels = labels)

specific_range1 <- setHighLight(28111017,28127138,"alpha")
custom_track <- drawArchs(ranges_list = custom_ranges, highlight_range_list = list(specific_range1))
tracks(custom_track) + xlim(current_range)

The resulting track is the fusion of track 1, 2 and 4 renamed "Chiapet 1", following by of track 3 and 5 renamed "Chiapet 2", the nineth track renamed "HiC 2" and then the seventh track with its original label.

andronekomimi/SNPVizualTools documentation built on May 10, 2019, 11:43 a.m.