calculates the distance of tracks values from intervals
bins the distances based on dist_breaks, and then calculates the average
methylation m / (m + um) in each bin and plots the results.
gpatterns.spatial_meth_trend(tracks, intervals, method = "extract",
dist_breaks = c(-4000000, -1000000, seq(-1000, 1000, 50), 1000000, 4000000),
iterator = .gpatterns.genome_cpgs_intervals, min_cov = NULL,
min_cgs = NULL, names = NULL, include.lowest = TRUE, groups = NULL,
group_name = NULL, add_vline = TRUE, ncol = 2, nrow = 2, width = 5,
height = 4, units = "in", pointsize = 12, res = 150, fig_fn = NULL,
xlab = "Distance (bp)", ylim = c(0, 1), linewidth = 0.8, title = "",
legend = TRUE, colors = NULL,
parallel = getOption("gpatterns.parallel"))
Arguments
- tracks
- tracks to plot
- intervals
- intervals to plot spatial methylation around.
Can be any intervals set, or one of the following 'special' intervals:
'tss', 'exon', 'utr3', 'intron', 'cgi'
- dist_breaks
- breaks to determine the distances from intervals
- iterator
- track expression iterator (of both tracks and strat_track)
- min_cov
- minimal coverage of each track
- min_cgs
- minimal number of CpGs per bin.
- names
- alternative names for the track
- include.lowest
- if 'TRUE', the lowest value of the range determined by breaks is included
- groups
- a vector the same length of
tracks with group for each track. Each group will on a different facet.
- group_name
- name of the grouping variable (e.g. tumor, sample, patient, experiment)
- add_vline
- add vertical line at 0 coordinate
- ncol
- number of columns
- nrow
- number of rows
- width
- plot width (if fig_fn is not NULL)
- height
- plot height (if fig_fn is not NULL)
- units
- see
png
- pointsize
- see
png
- res
- see
png
- fig_fn
- output filename for the figure (if NULL, figure would be returned)
- xlab
- label for the x axis'
- ylim
- ylim of the plot
- title
- title for the plot
- legend
- add legend
- colors
- custom colors
- parallel
- get trends parallely
Value
list with trend data frame (under 'trend') and the plot (under 'p')