logo_pssm {Logolas} | R Documentation

## Function to plot PSSM logo plot visualization.

### 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))

[Package Logolas version 1.11.0 Index]