ssvSignalLineplot: construct line type plots where each region in each sample is...

Description Usage Arguments Value Examples

View source: R/functions_signal_plots.R

Description

construct line type plots where each region in each sample is represented

Usage

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ssvSignalLineplot(bw_data, x_ = "x", y_ = "y", color_ = "sample",
  sample_ = "sample", region_ = "id", group_ = "auto_grp",
  line_alpha = 1, facet_ = "auto_facet", facet_method = facet_wrap,
  spline_n = NULL, return_data = FALSE)

Arguments

bw_data

a GRanges or data.table of bigwig signal. As returned from ssvFetchBam and ssvFetchBigwig

x_

variable name mapped to x aesthetic, x by default.

y_

variable name mapped to y aesthetic, y by default.

color_

variable name mapped to color aesthetic, sample by default.

sample_

variable name, along with region_ used to group and facet by default, change group_ or facet_ to override.

region_

variable name, along with sample_ used to group and facet by default, change group_ or facet_ to override.

group_

group aesthetic keeps lines of geom_path from mis-connecting. auto_grp by default which combines sample_ and region_. probably shouldn't change.

line_alpha

alpha value for lines. default is 1.

facet_

facetting divides up plots. auto_facet by default which combines sample_ and region_. if overriding facet_method with facet_grid, make sure to include ~ between two variables, ie. "a~b", ".~b", "a~."

facet_method

ggplot2 facetting method or wrapper for same, facet_wrap by default.

spline_n

if not NULL, applySpline will be called with n = spline_n. default is NULL.

return_data

logical. If TRUE, return value is no longer ggplot and is instead the data used to generate that plot. Default is FALSE.

Value

ggplot of signal potentially facetted by region and sample

Examples

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bw_gr = CTCF_in_10a_profiles_gr
ssvSignalLineplot(subset(bw_gr, bw_gr$id %in% seq_len(3)), facet_ = "sample")
ssvSignalLineplot(subset(bw_gr, bw_gr$id %in% seq_len(3)),
    facet_ = "sample~.",
    facet_method = facet_grid)
ssvSignalLineplot(subset(bw_gr, bw_gr$id %in% seq_len(3)),
    facet_ = paste("sample", "~", "id"), facet_method = facet_grid)
ssvSignalLineplot(subset(bw_gr, bw_gr$id %in% seq_len(3)))
ssvSignalLineplot(subset(bw_gr, bw_gr$id %in% seq_len(3)), facet_ = "id")
ssvSignalLineplot(subset(bw_gr, bw_gr$id %in% seq_len(3)),
    facet_ = "id", spline_n = 10)

jrboyd/seqsetvis documentation built on Oct. 28, 2018, 3:16 a.m.