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

In jrboyd/seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

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

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

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

data(CTCF_in_10a_profiles_gr)
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. 10, 2024, 11:23 a.m.