logo_pssm: Function to plot PSSM logo plot visualization.

Description Usage Arguments Value Examples

View source: R/logo_pssm.R

Description

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

Usage

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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

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

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