barAnno

Source: R/barAnno.R

Function for ChIP-seq and ATAC-seq. It must be used after the function annotatePeak() from the R package ChIPseeker. @seealso `annotatePeak` It takes a list of annotation objects that come as output of annotatePeak() and changes the features to "Promoter", "Distal" and "Gene body" (or to "Promoter" and "Distal"). Finally it plots a bargraph with the distribution of all the proportions As a ggplot2-based function, it allows to add more layers to format the plot.

barAnno(
  anno_list,
  anno_names = names(anno_list),
  names_order = unique(anno_names),
  protein = NULL,
  protein_order = unique(protein),
  main = NULL,
  subtitle = NULL,
  ylab = NULL,
  xlab = NULL,
  color_palette = "Set2",
  legend_position = "right",
  anno_num = 2,
  fill_position = T,
  xangle = 20,
  width = 0.6,
  counts_label = F,
  counts_angle = 90,
  counts_size = 3
)

Arguments

anno_list

Named list of annotation objects that come from annotatePeak().

anno_names

Charachter vector of the same length as 'anno_list'. Names that will be given to each of the objects in anno_list. Not that will be the names plotted in the bargraph

names_order

Character vector with the same entries as 'names' with the order wanted to plot the data. Defaults to: unique(names).

protein

NULL or haracter vector of the same length as 'anno_list' with the protein chipped in each dataframe of anno_list. If not NULL, these names will be passed through facet_wrap(). Default: NULL.

protein_order

Character vector with the same entries as 'protein' with the order wanted to plot the data. Defaults to: unique(protein).

main

Character of lenght 1. Title of the plot. Default: NULL.

subtitle

Character of lenght 1. Subtitle of the plot. Default: NULL.

ylab

Character of lenght 1. Title of the Y axis. Default: NULL.

xlab

Character of lenght 1. Title of the X axis. Default: NULL

legend_position

Character of lenght 1. Position of the legend. One of c("none", "bottom", "right", "left," "top"). Default: "right"

anno_num

Numerical or character of length 1. Number of annotations to plot, either 2 (Promoter/Distal), 3 (Promoter/Gene body/Distal) or 'all' (the annotatePeak() default). Default: 2.

fill_position

Logical. If TRUE (default), it the plotted bars will represent proportion of peaks in each feature. If FALSE, the bars will have the height of the total number of peaks with the correspondent feature color.

xangle

Numerical of length 1. Angle of the text in the X axis. Default: 20.

width

Numerical of length 1. Width of the bar in relative units. Default: 0.6

counts_label

Logical of length 1. Whether to write the number and percentage of observations in each annotation. Default: FALSE.

counts_angle

Numerical of length 1. Angle of the number and percentage labels. Default: 90

counts_size

Numerical of length 1. Size of the number and percentage labels. Default: 3

palette

Character of lenght 1. Color palette used to color the bars through the function scale_fill_brewer(). Default: "Set1".

Author

amitjavilaventura