// DNA_logo
// D. Thiebaut
// This program creates a DNA-sequence logo
// It uses 4 images for the 4 symbols A, C, G, and T, a.png, c.png, g.png
// and t.png. The images have black background and are captured from the
// display generated by the function generateACGTbitmaps()
//
// The program reads several sequences of identical length that reprensent
// potential binding regions between two strands, and calculates
// the frequency of each symbol appearing in each position of the consensus
// sequence, along with the information present in each symbol of the consensus
// string. The maximum value is 2 bits.
// This program assumes that each symbol is equally likely to appear in each
// position of the sequence.
//
// The symbols are shown with their height proportional to their frequency and
// the amount of information in each position.
//---------------------------------------------------------------------
// GEOMETRY
//---------------------------------------------------------------------
int WIDTH = 800; // width of the window in pixels
int MIDWIDTH = WIDTH/2; // half that
int HEIGHT = 600; // height, in pixels.
int BORDER = 40; // border around the window where nothing
// is displayed
int TITLELINE = 20; // y position of title line from top
int ALINE = HEIGHT/2; // y position of line where logo appears
PFont font; // the font used to display the symbols
int NOSEQS = 8; // number of sequences
float Afreq[]; // frequency of A symbols in sequences
float Cfreq[]; // C
float Gfreq[]; // G
float Tfreq[]; // T
float information[]; // amount of information at each location
// of the consensus sequence
String seq[] = new String[NOSEQS]; // array of sequences
//---------------------------------------------------------------------
// INITWINDOW: Draw the fixed text in the window
//---------------------------------------------------------------------
void initWindow( String title ) {
font = loadFont( "GillSans-60.vlw" ); // 60 points... very large!
textFont( font );
color myColor = color( 99, 66, 204 ); // font color
fill( myColor );
textSize( 24 ); // shrink for title
text( title, BORDER, TITLELINE ); // show title
}
//---------------------------------------------------------------------
// SETUP: called once when app starts.
//---------------------------------------------------------------------
void setup() {
size( WIDTH, HEIGHT );
background( 0, 0, 0 ); // black background
initWindow( "Sequence Logo" );
//--- initialize all 8 sequences ---
seq[0] = "CCCATTGTTCTC";
seq[1] = "TTTCTGGTTCTC";
seq[2] = "TCAATTGTTTAG";
seq[3] = "CTCATTGTTGTC";
seq[4] = "TCCATTGTTCTC";
seq[5] = "CCTATTGTTCTC";
seq[6] = "TCCATTGTTCGT";
seq[7] = "CCAATTGTTTTG";
//--- generate arrays of frequencies and information ---
int noSymbols = seq[0].length( );
Afreq = new float[ noSymbols ];
Cfreq = new float[ noSymbols ];
Gfreq = new float[ noSymbols ];
Tfreq = new float[ noSymbols ];
information = new float[ noSymbols ];
//--- compute information at each position of sequence ---
findFreqsAndInformation();
//--- display the logo ---
displayLogo();
}
//---------------------------------------------------------------------
// GENERATEACGTBITMAPS: use only when new png files needed
//---------------------------------------------------------------------
void generateACGTbitmaps() {
textSize( 60 );
fill( 255, 204, 0 );
text( "ACGT", BORDER, BORDER+60 );
fill( 132, 99, 0 );
text( "ACGT", BORDER, BORDER+60*2 );
fill( 99, 132, 204 );
text( "ACGT", BORDER, BORDER+60*3 );
fill( 99, 204, 33 );
text( "ACGT", BORDER, BORDER+60*4 );
}
//---------------------------------------------------------------------
// xlog2x: returns x * log( x )/log( 2 ) which would return NaN if
// not testing for 0 condition...
//---------------------------------------------------------------------
float xlog2x( float x ) {
if ( x==0 ) return 0; // because 0 * log( 0 ) is 0
return x * log(x)/log(2);
}
//---------------------------------------------------------------------
// fubdFreqsAndInformation: given the sequences, computes the frequency
// with which each symbol appears in each position, along with the
// information present in each symbol being the right one for that
// position.
//---------------------------------------------------------------------
void findFreqsAndInformation() {
//--- count how many times each ---
int noSymbols = seq[0].length( );
int Acount[] = new int[noSymbols ];
int Ccount[] = new int[noSymbols ];
int Gcount[] = new int[noSymbols ];
int Tcount[] = new int[noSymbols ];
//--- compute counts of A, C, G, and T in sequences ---
for ( int i=0; i<seq[0].length(); i++ ) {
Acount[i] = 0;
Ccount[i] = 0;
Gcount[i] = 0;
Tcount[i] = 0;
for ( int j=0; j<NOSEQS; j++ ) {
if ( seq[j].charAt(i)=='A' ) Acount[i] += 1;
if ( seq[j].charAt(i)=='C' ) Ccount[i] += 1;
if ( seq[j].charAt(i)=='G' ) Gcount[i] += 1;
if ( seq[j].charAt(i)=='T' ) Tcount[i] += 1;
}
}
//--- compute information in each place ---
for ( int i=0; i<seq[0].length(); i++ ) {
Afreq[i] = Acount[i]*1.0/ NOSEQS;
Cfreq[i] = Ccount[i]*1.0/ NOSEQS;
Gfreq[i] = Gcount[i]*1.0/ NOSEQS;
Tfreq[i] = Tcount[i]*1.0/ NOSEQS;
information[i] = 2.0 + xlog2x(Afreq[i])
+xlog2x( Cfreq[i] ) + xlog2x( Gfreq[i] )
+ xlog2x( Tfreq[i] );
//println( "information["+i+"] = "+information[i] );
}
}
//---------------------------------------------------------------------
// displayLogo: displays the logo in the window, at y = ALINE.
// Goes through all the possible symbol location and
// stack up the 4 images for the A, C, G, and T symbols
// where the height of the image is scaled by the information
// present in the consensus sequence, and by the frequency
// of each symbol. Maximum height is 2 bits.
//---------------------------------------------------------------------
void displayLogo() {
PImage a, c, g, t; // the 4 images of the 4 symbols
a = loadImage( "a.png" ); // load them from file into variables
c = loadImage( "c.png" );
g = loadImage( "g.png" );
t = loadImage( "t.png" );
//--- compute geometrical information ---
int noSymbols = seq[0].length();
float charWidth = (WIDTH-BORDER*2)/noSymbols;
char symbols[] = { 'A', 'C', 'G', 'T' };
//--- for each symbol position...
for ( int i=0; i< noSymbols; i++ ) {
float charBase = ALINE;
//--- for each possible symbol ...
for ( int j=0; j<4; j++ ) {
char sym = symbols[j];
PImage img;
float freq;
img = a; freq = Afreq[i];
if ( sym=='G' ) { img = g; freq = Gfreq[i]; }
if ( sym=='C' ) { img = c; freq = Cfreq[i]; }
if ( sym=='T' ) { img = t; freq = Tfreq[i]; }
float charHeight = 50 * information[i] * freq;
image( img, BORDER + i*charWidth, charBase-charHeight, charWidth, charHeight );
//--- change the y location for the base of the next image for stacking effect==>
charBase = charBase - charHeight;
}
}
}
