ssvSignalScatterplot {seqsetvis} | R Documentation |
maps signal from 2 sample profiles to the x and y axis. axes are standard or "volcano" min XY vs fold-change Y/X
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)
bw_data |
a GRanges or data.table of bigwig signal.
As returned from |
x_name |
sample name to map to x-axis, must be stored in variable specified in |
y_name |
sample name to map to y-axis, must be stored in variable specified in |
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 |
value_function |
a function to apply to |
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. |
ggplot of points comparing signal from 2 samples
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)