gfr2images.c

#include "log.h"
#include "format.h"
#include "geneFusionsConfig.h"
#include "gfr.h"
#include "gd.h"
#include "gdfontmb.h"
#include "gdfonts.h"
#include "gdfontt.h"


#define IMAGE_HEIGHT 200
#define MIN_IMAGE_WIDTH 600
#define SIDE_MARGIN 10
#define Y_COORDINATE_TRANSCRIPT_1 50
#define Y_COORDINATE_TRANSCRIPT_2 150
#define SPACER 12 // number of pixels between exons
#define EXON_SIZE 6 // number of pixels along the side of a square 



static void drawTranscript (int numberExons, int yCoordinateTranscript, gdImagePtr im, int color)
{
  int i;
  int xEndCoordinateTranscript;

  xEndCoordinateTranscript = SIDE_MARGIN + numberExons * EXON_SIZE + (numberExons + 1) * SPACER;
  gdImageLine(im,SIDE_MARGIN,yCoordinateTranscript,xEndCoordinateTranscript,yCoordinateTranscript,color);
  for (i = 1; i <= numberExons; i++) {
    gdImageFilledRectangle(im,
                           SIDE_MARGIN + i * SPACER + (i - 1) * EXON_SIZE,
                           yCoordinateTranscript - EXON_SIZE / 2,
                           SIDE_MARGIN + i * SPACER + (i - 1) * EXON_SIZE + EXON_SIZE,
                           yCoordinateTranscript + EXON_SIZE / 2,
                           color);
  }
}

void drawNumbers(gdImagePtr im, int numExons, int color) {
  int i;
  Stringa buffer = stringCreate(3);
  for( i=1; i<=numExons; i++) {
    stringPrintf( buffer, "%d", i);
    gdImageString( im, gdFontGetTiny(), 
                   SIDE_MARGIN + i * SPACER  + EXON_SIZE * i - EXON_SIZE / 2 - strlen(string(buffer)) * gdFontGetTiny()->w / 2,  
                   im->sy / 2,  
                   (unsigned char*) string(buffer), color);
  }
  stringDestroy(buffer);
}

static void makeImage (GfrEntry *currGE)
{
  gdImagePtr im;
  FILE *jpegout;
  int black,white, gray, blue, orange, green, color;
  int maxNumberExons;
  int imageWidth;
  int i;
  int xCoord1, xCoord2;
  //GfrInterRead *currGIR;
  static Stringa buffer = NULL;

  maxNumberExons = MAX (currGE->numExonsTranscript1,currGE->numExonsTranscript2);
  imageWidth = MAX (maxNumberExons * EXON_SIZE + (maxNumberExons + 1) * SPACER + 2 * SIDE_MARGIN,MIN_IMAGE_WIDTH);
  im = gdImageCreate(imageWidth,IMAGE_HEIGHT);
  white = gdImageColorAllocate(im,255,255,255);
  gray  = gdImageColorAllocate(im,192,192,192);
  blue  = gdImageColorAllocate(im,0,0,255);
  black = gdImageColorAllocate(im,0,0,0);
  orange = gdImageColorAllocate(im,255,69,0);
  green = gdImageColorAllocate(im, 46,139,87);

  gdImageString (im,gdFontGetMediumBold (),SIDE_MARGIN,Y_COORDINATE_TRANSCRIPT_1 - 30,(unsigned char*)currGE->geneSymbolTranscript1,black);
  gdImageString (im,gdFontGetMediumBold (),SIDE_MARGIN,Y_COORDINATE_TRANSCRIPT_2 + 18,(unsigned char*)currGE->geneSymbolTranscript2,black);
  drawTranscript (currGE->numExonsTranscript1,Y_COORDINATE_TRANSCRIPT_1,im,black);
  drawTranscript (currGE->numExonsTranscript2,Y_COORDINATE_TRANSCRIPT_2,im,black);
  drawNumbers ( im, MAX( currGE->numExonsTranscript1, currGE->numExonsTranscript2), black);
  for( i = 0; i< arrayMax( currGE->pairCounts); i++ ) {
    GfrPairCount* currGEPC = arrp( currGE->pairCounts, i, GfrPairCount);
    switch( currGEPC->pairType ) {
    case GFR_PAIR_TYPE_EXONIC_EXONIC:
      xCoord1 = SIDE_MARGIN + currGEPC->number1 * SPACER + currGEPC->number1 * EXON_SIZE - EXON_SIZE / 2;
      xCoord2 = SIDE_MARGIN + currGEPC->number2 * SPACER + currGEPC->number2 * EXON_SIZE - EXON_SIZE / 2;
      color = orange;
      break;
    case GFR_PAIR_TYPE_EXONIC_INTRONIC:
      xCoord1 = SIDE_MARGIN + currGEPC->number1 * SPACER + currGEPC->number1 * EXON_SIZE - EXON_SIZE / 2;
      xCoord2 = SIDE_MARGIN + currGEPC->number2 * SPACER + currGEPC->number2 * EXON_SIZE + SPACER / 2;
      color = orange;
      break;
    case GFR_PAIR_TYPE_EXONIC_JUNCTION:
      xCoord1 = SIDE_MARGIN + currGEPC->number1 * SPACER + currGEPC->number1 * EXON_SIZE - EXON_SIZE / 2;
      xCoord2 = SIDE_MARGIN + (currGEPC->number2/2) * SPACER + (currGEPC->number2)/2 * EXON_SIZE + (currGEPC->number2 % 2) * SPACER;
      color = orange;
      break;    
    case GFR_PAIR_TYPE_INTRONIC_EXONIC:
      xCoord1 = SIDE_MARGIN + currGEPC->number1 * SPACER + currGEPC->number1 * EXON_SIZE + SPACER / 2;
      xCoord2 = SIDE_MARGIN + currGEPC->number2 * SPACER + currGEPC->number2 * EXON_SIZE - EXON_SIZE / 2;
      color = green;
      break;
     case GFR_PAIR_TYPE_INTRONIC_INTRONIC:
      xCoord1 = SIDE_MARGIN + currGEPC->number1 * SPACER + currGEPC->number1 * EXON_SIZE + SPACER / 2;
      xCoord2 = SIDE_MARGIN + currGEPC->number2 * SPACER + currGEPC->number2 * EXON_SIZE + SPACER / 2;
      color = green;
      break; 
    case GFR_PAIR_TYPE_INTRONIC_JUNCTION:
      xCoord1 = SIDE_MARGIN + currGEPC->number1 * SPACER + currGEPC->number1 * EXON_SIZE + SPACER / 2;
      xCoord2 = SIDE_MARGIN + (currGEPC->number2/2) * SPACER + (currGEPC->number2)/2 * EXON_SIZE + (currGEPC->number2 % 2) * SPACER;
      color = green;
      break;     
    case GFR_PAIR_TYPE_JUNCTION_JUNCTION:
      xCoord1 = SIDE_MARGIN + (currGEPC->number1/2) * SPACER + (currGEPC->number1) / 2 * EXON_SIZE + (currGEPC->number1 % 2) * SPACER;
      xCoord2 = SIDE_MARGIN + (currGEPC->number2/2) * SPACER + (currGEPC->number2) / 2 * EXON_SIZE + (currGEPC->number2 % 2) * SPACER;
      color = gray;
      break;     
    case GFR_PAIR_TYPE_JUNCTION_EXONIC:
      xCoord1 = SIDE_MARGIN + (currGEPC->number1/2) * SPACER + (currGEPC->number1) / 2 * EXON_SIZE + (currGEPC->number1 % 2) * SPACER;
      xCoord2 = SIDE_MARGIN + currGEPC->number2 * SPACER + currGEPC->number2 * EXON_SIZE - EXON_SIZE / 2;
      color = gray;
      break;     
    case GFR_PAIR_TYPE_JUNCTION_INTRONIC:
      xCoord1 = SIDE_MARGIN + (currGEPC->number1/2) * SPACER + (currGEPC->number1) / 2 * EXON_SIZE + (currGEPC->number1 % 2) * SPACER;
      xCoord2 = SIDE_MARGIN + currGEPC->number2 * SPACER + currGEPC->number2 * EXON_SIZE + SPACER / 2;
      color = gray;
      break;     
    default:
      xCoord1 = SIDE_MARGIN;
      xCoord2 = SIDE_MARGIN;
      color = white;
      break;
    }
    gdImageLine(im,
                xCoord1,
                Y_COORDINATE_TRANSCRIPT_1,
                xCoord2,
                Y_COORDINATE_TRANSCRIPT_2,
                color);
  }
  /*  for (i = 0; i < arrayMax (currGE->interReads); i++) {
      currGIR = arrp (currGE->interReads,i,GfrInterRead);
      gdImageLine(im,
      xCoord1,
      Y_COORDINATE_TRANSCRIPT_1,
      xCoord2,
      Y_COORDINATE_TRANSCRIPT_2,
      color);
    //    gdImageLine(im,
    //             SIDE_MARGIN + currGIR->exonNumber1 * SPACER + (currGIR->exonNumber1 - 1) * EXON_SIZE + EXON_SIZE / 2,
    //             Y_COORDINATE_TRANSCRIPT_1,
    //             SIDE_MARGIN + currGIR->exonNumber2 * SPACER + (currGIR->exonNumber2 - 1) * EXON_SIZE + EXON_SIZE / 2,
    //             Y_COORDINATE_TRANSCRIPT_2,
    //             black);
    }
    //*/
  stringCreateClear (buffer,100);
  stringPrintf (buffer,"%s.jpg",currGE->id);
  jpegout = fopen(string (buffer), "wb");
  gdImageJpeg(im, jpegout, -1);
  fclose(jpegout);
  gdImageDestroy(im); 
}



int main (int argc, char *argv[])
{
  GfrEntry *currGE;
  int count;

  count = 0;
  gfr_init ("-");
  puts (gfr_writeHeader ());
  while (currGE = gfr_nextEntry ()){
    makeImage (currGE);
    puts (gfr_writeGfrEntry (currGE));
    count++;
  }
  gfr_deInit ();
  warn ("%s_numGfrEntries: %d",argv[0],count);
  return 0;
}

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