| ## RNAstructure Command Line Help ProbabilityPlot | ### Contents ### Index
ProbabilityPlot is used to create a base pairing probabilities plot after calculating the partition function (which can be done using the partition interface). The plot has nucleotide index (position, 1-indexed) on x axis and nucleotide index on the y axis. A dot is a possible base pair, with its probability coded in color. Plots and text show the -log10(probability). ### USAGE: ProbabilityPlot <input file> <output file> [options] ### Required parameters:
<input file> | The name of the input file that holds base pairing probabilities. This file may be one of the following file types. 1) Partition function save file (binary file). (The default file type.) Generated by the program partition. 2) Matrix file (plain text). Note that in order to use a matrix file, the "--matrix" flag must be specified (see "--matrix" below). 3) Dot plot file (plain text). This file is in the standard format exported by ProbabilityPlot when the "--text" option is used. Note that in order to use a dot plot file, the "--log10" flag must be specified.
<output file> | The name of a file to which output will be written. Depending on the options selected, this may be one of the following file types. 1) A Postscript image file (default). 2) An SVG image file (use --svg flag). 3) A plain text file (use --text flag).
### Options that do not require added values:
-h, -H, --help | Display the usage details message.
--matrix | Indicate that the input file is a plain text matrix of pairing probabilities rather than a partition function save file. This text file is generated by partition-cuda.
-s, -S, --stack | Calculate the probability that a pair exists and is stacked between two adjacent pairs. This requires that the input file is a binary partition function save file.
| --log10 | Specifies that the input file format is a dot plot text file of log10 base pair probabilities. (This file format is the output file format used for when --text flag is given.)
--svg | Specify that the output file should be an SVG image file, rather than a Postscript image file.
-t, -T, --text | Write dot plot as a text file, rather than a Postscript image file.
-v, --version | Display version and copyright information for this interface.

### Options that require added values:

--desc | Configure the output of descriptions. Valid values are: (1) "" or "~none" -- Do not write a description (2) "~file" -- If the default description corresponds to a file or path, use only the base name of the path (i.e. no directory or file extension). (3) "~~" or "~default" -- Use the default description (this is the same as not specifying the flag) (4)"~list|DESC1|DESC2|DESC3" -- use this syntax when the output is expected to have more than one plot. It specifies a list of descriptions will be applied in the order given. The character immediately after "~list" will be used as the separator (i.e. it need not be the bar (|) character. (5) Any other value is assumed to be the literal description you want to have displayed in the plot legend.
-e, -E, --entries | Specify the number of categories in the plot legend. Default is 5 colors. Minimum is 3 colors. Maximum is 15 colors.
-max, -MAX, --maximum | Specify the maximum value in the plot in -log10(probability). Default is the largest valid value in the plot.
-min, -MIN, --minimum | Specify the minimum value in the plot in -log10(probability). Default is the smallest valid value in the plot.

### References:

1. Reuter, J.S. and Mathews, D.H.
   "RNAstructure: software for RNA secondary structure prediction and analysis."
   BMC Bioinformatics, 11:129. (2010).
2. Mathews, D.H.
   "Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization."
   RNA, 10:1178-1190. (2004).
3. McCaskill, J.S.
   "The equilibrium partition function and base pair probabilities for RNA secondary structure."
   Biopolymers, 29:1105-1119. (1990).