ssvSignalScatterplot: maps signal from 2 sample profiles to the x and y axis. axes...

Description Usage Arguments Value Examples

View source: R/functions_signal_plots.R

Description

maps signal from 2 sample profiles to the x and y axis. axes are standard or "volcano" min XY vs fold-change Y/X

Usage

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ssvSignalScatterplot(bw_data, x_name, y_name, color_table = NULL,
  value_variable = "y", xy_variable = "sample", value_function = max,
  by_ = "id", plot_type = c("standard", "volcano")[1],
  show_help = FALSE, fixed_coords = TRUE, return_data = FALSE)

Arguments

bw_data

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

x_name

sample name to map to x-axis, must be stored in variable specified in xy_variable

y_name

sample name to map to y-axis, must be stored in variable specified in xy_variable

color_table

data.frame with 2 columns, one of which must be named "group" and gets mapped to color. The other column must be the same as by_ parameter and is used for merging.

value_variable

variable name that stores numeric values for plotting, default is "y"

xy_variable

variable name that stores sample, must contain entires for x_name and y_name

value_function

a function to apply to value_variable in all combintations of by_ per x_name and y_name

by_

variables that store individual measurement ids

plot_type

standard or volcano, default is "standard"

show_help

if TRUE overlay labels to aid plot interpretation, default is FALSE

fixed_coords

if TRUE coordinate system is 1:1 ratio, default is TRUE

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 points comparing signal from 2 samples

Examples

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ssvSignalScatterplot(CTCF_in_10a_profiles_gr,
    x_name = "MCF10A_CTCF", y_name = "MCF10AT1_CTCF")
ssvSignalScatterplot(CTCF_in_10a_profiles_gr,
    x_name = "MCF10A_CTCF", y_name = "MCF10CA1_CTCF")

ssvSignalScatterplot(CTCF_in_10a_profiles_gr,
    x_name = "MCF10A_CTCF", y_name = "MCF10AT1_CTCF",
    value_function = median) + labs(title = "median FE in regions")

ssvSignalScatterplot(CTCF_in_10a_profiles_gr,
    x_name = "MCF10A_CTCF", y_name = "MCF10AT1_CTCF",
    plot_type = "volcano")

ssvSignalScatterplot(CTCF_in_10a_profiles_gr,
    x_name = "MCF10A_CTCF", y_name = "MCF10AT1_CTCF",
    plot_type = "volcano", show_help = TRUE)

jrboyd/seqsetvis documentation built on Dec. 15, 2018, 1:26 a.m.