damageLogo_five: Builds damage logo plots along with mutational profile across...

In kkdey/aRchaic.site: Visualization, Exploration and Clustering of Ancient vs Modern BAM mutation patterns

Description

Damage Logo plots for each cluster representing the substitution frequency of the 6 substitutional patterns (adjusting for strand bias) and the flanking bases arranged as per relative frequency on either side of the substitution along with the probability of the cluster mutational profile along the read and the strand break composition.

Usage

damageLogo_five(theta_pool, sig_names = NULL, ic.scale = TRUE,
  max_pos = 20, flanking_bases = 1, yscale_change = TRUE, xaxis = TRUE,
  yaxis = TRUE, xlab = " ", xaxis_fontsize = 5, xlab_fontsize = 10,
  y_fontsize = 10, mut_width = 2, start = 1e-04, renyi_alpha = 1,
  pop_names = paste0("Cluster ", 1:dim(theta_pool)[2]), logoport_x = 0.28,
  logoport_y = 0.5, logoport_width = 0.3, logoport_height = 0.4,
  lineport_x = 0.72, lineport_y = 0.34, lineport_width = 0.25,
  lineport_height = 0.25, breaklogoport_x = 1, breaklogoport_y = 0.4,
  breaklogoport_width = 0.4, breaklogoport_height = 0.5, barport_x = 0.6,
  barport_y = 0.6, barport_width = 0.3, barport_height = 0.25)

Arguments

theta_pool	The theta matrix obtained from running the grade of membership model that stores for each cluster, the probability distribution over all the mutational signatures.
sig_names	The mutational signature names. Defaults to the rownames of the theta matrix above.
ic.scale	A binary variable indicating whether the height of the bars for substitution and flanking bases should be adjusted by the information criterion.
max_pos	The maximum distance from the end of the read upto which mutations are considered.
flanking_bases	The number of flanking bases of the mutational signature.
yscale_change	A binary variable indicating whether the Y axis scale should be adjusted based on the size of the logos, defaults to TRUE.
xaxis	A binary indicating whether the X axis of the logo plot should be shown
yaxis	A binary indicating whether the Y axis of the logo plot should be shown
xlab	The labels for X axis.
xaxis_fontsize	The fontsize of the X axis ticks.
xlab_fontsize	The fontsize of the X axis labels.
y_fontsize	The fontsize of the Y axis ticks.
mut_width	Thw width of the bar for the mutation at the center.
start	The starting point of the stacking of logos on the Y axis. Should be close to 0, defau;ts to 0.0001.
renyi_alpha	The entropy scale for the Renyi entropy on the flanking bases and mutations.
pop_names	The title of the plot. Defaults to the cluster labels.
logoport_x	the X-axis position of the plot window for the logo plot
logoport_y	the Y-axis position of the plot window for the logo plot
logoport_width	the width of the plot window for the logo plot
logoport_height	the width of the plot window for the logo plot
lineport_x	the X-axis position of the plot window for the mutational profile line plot.
lineport_y	the Y-axis position of the plot window for the mutational profile line plot.
lineport_width	the width of the plot window for the mutational profile line plot.
lineport_height	the width of the plot window for the mutational profile line plot.

Value

Returns logo plots for each cluster

kkdey/aRchaic.site documentation built on May 20, 2019, 10:31 a.m.