plotBaseModificationProf: plotBaseModificationProf

In MingLi-929/BMplot: BMplot for Base Modification Visulization

plotBaseModificationProf

Description

plot base modification profile

Usage

plotBaseModificationProf(
  df,
  motif_color = NULL,
  title = NULL,
  xlim = NULL,
  GeneModel = NULL,
  highlight_lim = NULL,
  highlight_color = NULL,
  highlight_alpha = 0.2,
  xlab = "Genomic Region(5'->3')",
  ylab = NULL,
  second_ylab = NULL,
  switch_y_value = FALSE,
  legend_lab_motif = NULL,
  legend_lab_value2 = NULL,
  switch_facet_label = TRUE,
  strip_placement = "outside",
  angle_of_facet_label = 0,
  alpha = 0.6,
  y_ticks_length = 0.25,
  x_ticks_length = 0.25,
  strip_border = FALSE,
  facet_label_text_size = 12,
  axis_title_text_size = 17,
  title_text_size = 20,
  right_y_axis_text_size = 13,
  left_y_axis_text_size = 13,
  x_axis_text_size = 13,
  depth_heatmap = TRUE,
  nrow = NULL,
  ncol = NULL,
  panel_spacing = 1,
  legend_box_spacing = 3,
  legend_position = "right"
)

Arguments

df	the base modification dataframe
motif_color	the color for different motifs(CHH,CHG,CG)
title	the title of the plot, can also be a list of title
xlim	the specified interval of region, must be the sub-interval of the dmR. list for list df
GeneModel	annotation data, can be TxDb/GRanges/GRangesList etc. Details see ggbio::autoplot()
highlight_lim	the high light region. list for list df
highlight_color	the color of high light rectangular box
highlight_alpha	the alpha of highlight box
xlab	the x label, can also be a list of x label
ylab	the y label, can also be a list of y label
second_ylab	the ylab for second y-axis
switch_y_value	switch the value from left y-axis to right y-axis
legend_lab_motif	the label of legend for motif
legend_lab_value2	the label of legend for the second value(ylab is the label for the first value)
switch_facet_label	switch the facet label from right to left or not
strip_placement	strip.placement
angle_of_facet_label	the angle of facet label, e.g. 0 is horizontal
alpha	transparency for the depth information line
y_ticks_length	the length of y-axis ticks
x_ticks_length	the length of x-axis ticks
strip_border	add border to the facet label or not
facet_label_text_size	the size of facet label text
axis_title_text_size	the size of axis title text
title_text_size	the size of the title text
right_y_axis_text_size	the size of the left y axis text,this work when depth information is taken into account
left_y_axis_text_size	the size of the left y axis text
x_axis_text_size	the size of x axis text
depth_heatmap	draw the heatmap of depth information or not
nrow	the nrow of plotting a list of dmR
ncol	the ncol of plotting a list of dmR
panel_spacing	the distance between panels
legend_box_spacing	the distance between legend and plotting area,"cm"
legend_position	the position of legend

Value

ggplot object

MingLi-929/BMplot documentation built on Dec. 11, 2024, 6:06 p.m.