void motifLogoAndMatrix(struct dnaSeq **seqs, int count, struct dnaMotif *motif)
/* Print out motif sequence logo and text (possibly with multiple occurences) */
{
// Detect inconsistent motif/pwm tables and suppress confusing display
if (motif != NULL)
{
if (seqs != NULL && motif->columnCount != seqs[0]->size)
{
warn("Motif seq length doesn't match PWM\n");
return;
}
}
#define MOTIF_HELP_PAGE "../goldenPath/help/hgRegMotifHelp.html"
printf("<PRE>\n");
printf("<table>\n");
if (motif != NULL)
{
struct tempName pngTn;
dnaMotifMakeProbabalistic(motif);
makeTempName(&pngTn, "logo", ".png");
dnaMotifToLogoPng(motif, 47, 140, NULL, "../trash", pngTn.forCgi);
printf("<tr><td></td><td colspan='%d'align=right><a href=\"%s\" target=_blank>Motif display help</a></td></tr>",
motif->columnCount, MOTIF_HELP_PAGE);
printf("<tr><td></td><td colspan='%d'>", motif->columnCount);
printf("<IMG SRC=\"%s\" BORDER=1>", pngTn.forHtml);
printf("</td><td></td></tr>\n");
}
if (count > 0)
{
int i;
for (i = 0; i < count; i++)
{
struct dnaSeq *seq = seqs[i];
printf("<tr><td></td>");
touppers(seq->dna);
printDnaCells(seq->dna, seq->size);
if (count == 1)
printf("<td>this occurrence</td></tr>\n");
else
// is there a library routine to get 1st, 2nd ...?
printf("<td>occurrence #%d</td></tr>\n", i + 1);
}
}
if (motif != NULL)
{
printf("<tr><td></td>");
printConsensus(motif);
printf("<td>motif consensus</td></tr>\n");
dnaMotifPrintProbTable(motif, stdout);
}
printf("</table>\n");
printf("</PRE>");
}
static void transRegCodeMotifPrint(struct section *section,
struct sqlConnection *conn, char *geneId)
/* Print out transcription regulatory code info. */
{
struct dnaMotif *motif = transRegMotif(conn, geneId);
if (motif != NULL)
{
struct tempName pngTn;
dnaMotifMakeProbabalistic(motif);
makeTempName(&pngTn, "logo", ".png");
dnaMotifToLogoPng(motif, 47, 140, NULL, "../trash", pngTn.forCgi);
hPrintf(" ");
hPrintf("<IMG SRC=\"%s\" BORDER=1>", pngTn.forHtml);
hPrintf("\n");
hPrintf("<PRE>");
dnaMotifPrintProb(motif, stdout);
hPrintf("</PRE><BR>\n");
hPrintf("This data is from ");
hPrintf("<A HREF=\"%s\" TARGET=_blank>",
"http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v431/n7004/abs/nature02800_fs.html");
hPrintf("Transcriptional regulatory code of a eukaryotic genome</A> ");
hPrintf("by Harbison, Gordon, et al.");
}
}
