Author: Zuguang Gu ( z.gu@dkfz.de )
Date: 2016-03-04
In gtrellis, genomic categories are not restricted in chromosomes. It can be any kind, such as genes, as long as the background ranges are specified.
In following example, we put three genes in one row and draw their transcripts afterwards.
In gtrellis package, tp_family.RData contains transcripts models for TP53, TP63 and TP73.
First we calculate the ranges for the three genes.
library(gtrellis)
load(system.file("extdata", "tp_family.RData", package = "circlize"))
df = data.frame(gene = names(tp_family),
start = sapply(tp_family, function(x) min(unlist(x))),
end = sapply(tp_family, function(x) max(unlist(x))))
df
## gene start end
## TP73 TP73 3569084 3652765
## TP63 TP63 189349205 189615068
## TP53 TP53 7565097 7590856
Since multiple transcripts are plotted stack by stack, the maximum number of transcripts for the three genes are calculated and it will be set as the maximum value on y-axis.
# maximum number of transcripts
n = max(sapply(tp_family, length))
n
## [1] 17
df contains ranges for the three genes and it can be passed to gtrellis_layout() for initializing the Trellis layout.
Since Trellis layout will be changed in later part of this document, the code for adding graphics are wrapped into a function
for repeatitive use.
gtrellis_layout(data = df, n_track = 1, track_ylim = c(0.5, n+0.5),
track_axis = FALSE, add_name_track = TRUE, xpadding = c(0.05, 0.05),
ypadding = c(0.05, 0.05))
plot_transcripts_model = function(tp_family) {
add_track(panel_fun = function() {
gn = get_cell_meta_data("name")
tr = tp_family[[gn]] # all transcripts for this gene
for(i in seq_along(tr)) {
# for each transcript
current_tr_start = min(tr[[i]]$start)
current_tr_end = max(tr[[i]]$end)
grid.lines(c(current_tr_start, current_tr_end), c(n - i + 1, n - i + 1),
default.units = "native", gp = gpar(col = "#CCCCCC"))
grid.rect(tr[[i]][[1]], n - i + 1, tr[[i]][[2]] - tr[[i]][[1]], 0.8,
default.units = "native", just = "left",
gp = gpar(fill = "orange", col = "orange"))
}
})
}
plot_transcripts_model(tp_family)
Next we change the layout into one-column layout. Now the coordinate for all three genes are changed to the relative positions to TSS because all three genes are aligned by their TSS on the plot. In following example, these 'magic numbers' are positions of the TSS of corresponding genes.
# TP53 is on reverse strand
tp_family$TP53 = lapply(tp_family$TP53, function(df) {
data.frame(start = 7590856 - df[[2]],
end = 7590856 - df[[1]])
})
tp_family$TP63 = lapply(tp_family$TP63, function(df) {
data.frame(start = df[[1]] - 189349205,
end = df[[2]] - 189349205)
})
tp_family$TP73 = lapply(tp_family$TP73, function(df) {
data.frame(start = df[[1]] - 3569084,
end = df[[2]] - 3569084)
})
df = data.frame(gene = names(tp_family),
start = sapply(tp_family, function(x) min(unlist(x))),
end = sapply(tp_family, function(x) max(unlist(x))))
df
## gene start end
## TP73 TP73 0 83681
## TP63 TP63 0 265863
## TP53 TP53 0 25759
Since only the layout is changed here, plot_transcripts_model() can be directly applied here.
n = max(sapply(tp_family, length))
gtrellis_layout(data = df, n_track = 1, ncol = 1, track_ylim = c(0.5, n+0.5),
track_axis = FALSE, add_name_track = TRUE,
xpadding = c(0.01, 0.01), ypadding = c(0.05, 0.05))
plot_transcripts_model(tp_family)
sessionInfo()
## R version 3.2.2 (2015-08-14)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: OS X 10.11.3 (El Capitan)
##
## locale:
## [1] C/en_US.UTF-8/C/C/C/C
##
## attached base packages:
## [1] stats4 parallel methods grid stats graphics grDevices
## [8] utils datasets base
##
## other attached packages:
## [1] gtrellis_1.3.3 GenomicRanges_1.20.8 GenomeInfoDb_1.4.3
## [4] IRanges_2.2.9 S4Vectors_0.6.6 BiocGenerics_0.14.0
##
## loaded via a namespace (and not attached):
## [1] circlize_0.3.4 formatR_1.2.1 magrittr_1.5
## [4] evaluate_0.8 GlobalOptions_0.0.8 stringi_1.0-1
## [7] XVector_0.8.0 GetoptLong_0.1.1 rjson_0.2.15
## [10] tools_3.2.2 stringr_1.0.0 colorspace_1.2-6
## [13] shape_1.4.2 knitr_1.11