Plot 4C nearcis profile.

Plot a nearcis profile in the defined genomic scope. Can be applied on a single p4cProfile object or a two object for a comparison plot.

# S3 method for p4cProfile
plot(p4c_obj1, p4c_obj2, trend_scale = "adaptive", png_fn = NULL, ...)

plotSingleProf(
  p4c_obj,
  trend_scale,
  png_fn,
  plot.colorbar,
  add.func,
  xlim,
  ylim,
  trend_only,
  main,
  sd,
  ...
)

plotCompProf(
  p4c_obj1,
  ref_p4c_obj,
  trend_scale,
  png_fn,
  col,
  min_win_cov,
  xlim,
  zlim,
  legend.text,
  ylim,
  dgram.method,
  main,
  sd
)

Arguments

p4c_obj1	p4cProfile object created by p4cNewProfile.
p4c_obj2	Optional. A second p4cProfile object that will be compared to p4c_obj1.
trend_scale	This parameter controls the smoothing method for the trendline. Either 'adaptive' (default), or, for fixed window trend, an integer with the desired size of the window (in restriction fragments units).
png_fn	File to save the plot to. The default (NULL) will result in plotting on the current graphic device.
plot.colorbar	Optional. Logical that defines whether a colorbar for the domainogram should be plotted.
xlim	Similar to R basic graphics. A two elements vector that controls the genomic focus of the plot (X axis).
ylim	Similar to R basic graphics. A two elements vector that controls the trendline ylim (In units of molecules).
trend_only	Optional. Logical that defines whether only the trend plot should be displayed.
main	Plot title.
sd	Controls the margins of the trendline. The Number of bionomial theoretical standard deviations.
col	Vector with length 2 that controls the colors of each profile in a comparative plot.
min_win_cov	If the default smoothing method is used ('adaptive'), this parameter controls the window size by requiring that no less than min_win_cov molecules will be included in that genomic window.
legend.text	Character vector with length 2. Controls the text in the color legend of the trendline. The default are the names of the profiles.
filename1	Optional. File for the bedgraph with the trendline of `p4c_obj1`
filename2	Optional. File for the bedgraph with the trendline of `p4c_obj2`

Details

This function calls two methods depending on whether it is called on a single object or two objects. When it is called on a single p4cProfile object it will produce a nearcis plot with smoothed trendline, and a contact intensity domainogram. Calling this function for two object will produce a comparison plot of where the 4C profiles are normalized for UMI coverage. The two p4cProfile objects must be constructed for the same bait with the same genomic scope.

Examples

# \donttest{
# Create a p4cProfile object:
fc <- p4cNewProfile("umi4C_example_CMK_ANK1_TSS")
#> Error in p4cNewProfile("umi4C_example_CMK_ANK1_TSS"): cannot find track umi4C_example_CMK_ANK1_TSS

# Plot a profile on:
plot(fc, xlim=c(41554693, 41754693), ylim=c(0, 5), plot.colorbar=TRUE)
#> Error in plot(fc, xlim = c(41554693, 41754693), ylim = c(0, 5), plot.colorbar = TRUE): object 'fc' not found


# Comparing two profiles:
# Create a second profile
fc_cond2 <- p4cNewProfile("umi4C_example_DND41_ANK1_TSS")
#> Error in p4cNewProfile("umi4C_example_DND41_ANK1_TSS"): cannot find track umi4C_example_DND41_ANK1_TSS

# Plot profiles
plot(fc, fc_cond2, col=c('red', 'blue'), min_win_cov=100, main = '4C figure', png_fn='fig.png') 
#> Error in plot(fc, fc_cond2, col = c("red", "blue"), min_win_cov = 100,     main = "4C figure", png_fn = "fig.png"): object 'fc' not found
# }