logo_pssm: Function to plot PSSM logo plot visualization.

In Logolas: EDLogo Plots Featuring String Logos and Adaptive Scaling of Position-Weight Matrices

Description

stacks logos created by the makemylogo function on top of each other to build the PSSM logo plot.

Usage

logo_pssm(table, color_type = NULL, colors = NULL, color_seed = 2030,
  total_chars = c("A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L",
  "M", "N", "O", "P", "Q", "R", "S", "T", "U", "V", "W", "X", "Y", "Z", "zero",
  "one", "two", "three", "four", "five", "six", "seven", "eight", "nine", "dot",
  "comma", "dash", "colon", "semicolon", "leftarrow", "rightarrow"),
  frame_width = NULL, yscale_change = TRUE, pop_name = NULL,
  addlogos = NULL, addlogos_text = NULL, newpage = TRUE, ylimit = NULL,
  xaxis = TRUE, yaxis = TRUE, xaxis_fontsize = 10, xlab_fontsize = 15,
  y_fontsize = 15, main_fontsize = 16, start = 0.001, xlab = "X",
  ylab = "PSSM  Score", col_line_split = "grey80", control = list())

Arguments

table	The input table (data frame or matrix) of PSSM scores (comprising of both positive and negative scores) across different logos or symbols (specified along the rows) and across different sites or positions or groups (specified along the columns).
color_type	A list specifying the coloring scheme. Defaults to NULL, for which, based on color_seed, a specific coloring scheme is chosen. The list contains two elements - type and col.The type can be of three types - "per-row", "per-column" and "per-symbol". The col element is a vector of colors, of same length as number of rows in table for "per-row" (assigning a color to each string), of same length as number of columns in table for "per-column" (assuming a color for each column), or a distinct color for a distinct symbol in "per-symbol". For "per-symbol", the length of the color_profile$col should be same as library size of the logos, but if the vector of colors provided is more or less, we can downsample or upsample the colors as required. The colors are matched with the symbols in the total_chars.
colors	Add description here.
color_seed	Add description here.
total_chars	The total number of character symbols in the user library. The default is the default library provided by Logolas, but the user can add symbols that he creates to this list.
frame_width	The width of the frames for individual site/postion/column in the logo plot. As default, all the columns have same width, equal to 1.
yscale_change	If TRUE, adjusts the Y axis scale based on the size of the bars, else keeps it to the maximum value possible, which is ceiling(max(ic) under ic_computer defined IC criteria.
pop_name	User can mention a name of the population for which the logo plot is created. Defaults to NULL when no population name is mentioned.
addlogos	Vector of additional logos/symbols defined by user
addlogos_text	Vector of the names given to the additional logos/symbols defined by user.
newpage	if TRUE, plots the logo plot in a new page. Defaults to TRUE.
ylimit	The limit of the Y axis.
xaxis	Binary specifying if there should be a X axis in the logo plot or not. Defaults to TRUE.
yaxis	Binary specifying if there should be a Y axis in the logo plot or not. Defaults to TRUE.
xaxis_fontsize	The size of the X-axis axis ticks.
xlab_fontsize	The size of the X-axis label.
y_fontsize	The size of the Y-axis font.
main_fontsize	The size of the title.
start	The starting point in Y axis for the first logo. Default is 0.0001 which is very close to 0.
xlab	X axis label
ylab	Y axis label
col_line_split	The color of the line split between the consecutive groups or blocks
control	control parameters fixing whether the symbols should be filled with color or border colored (tofill_pos, tofill_neg), the viewport configuration details for the plot (viewport.margin.bottom, viewport.margin.left, viewport.margin.top, viewport.margin.right) etc.

Value

Plots the logo plot for the PSSM scoring data, with column names representing the sites/blocks and the row names denoting the symbols for which logos are plotted

Examples

data(pssm)
logo_pssm(pssm, control = list(round_off = 0))

Logolas documentation built on April 28, 2020, 8:55 p.m.