/* usage - functions that display helpful usage info text go here. -jk)*/
/* Copyright (C) 2011 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "hPrint.h"
void printMainHelp()
/* Put up main page help info. */
{
hPrintf("%s",
"Genome Graphs is a tool for displaying genome-wide data sets such\n"
"as the results of genome-wide SNP association studies, linkage studies\n"
"and homozygosity mapping. This section provides line-by-line descriptions\n"
"of the controls on this page. For more detailed instructions, see the\n"
"Genome\n"
"Graphs User's Guide.\n"
"
\n"
" - clade: Specifies which clade the organism is in."
"
\n"
" - genome: Specifies which organism data to use."
"
\n"
" - assembly: Specifies which version of the organism's"
" genome sequence to use.\n"
"
\n"
" - graph ... in ...: Selects which graph(s) to display in "
" which color."
"
\n"
" - upload: Takes you to a page where you can upload your "
" own data.\n"
"
\n"
" - import: Takes you to a page where you can import "
" database tables from this assembly.\n"
"
\n"
" - configure: Takes you to a page where you can control "
" many aspects of the display including the overall size of the image, "
" how many graphs can be drawn, and the chromosome layout."
"
\n"
" - correlate: If more than one graph is selected, takes you "
" to a page listing the Pearson's correlation coefficient for each "
" pair of graphs."
"
\n"
" - significance threshold: Values above this threshold will "
" be considered significant. A light blue line will be drawn across "
" the graphs at the significance threshold of the first graph. Regions "
" above the threshold will be included in the region list you get with "
" the browse regions button."
"
\n"
" - browse regions: Takes you to a page with a list of all "
" regions above the significance threshold on the left, and a "
" Genome Browser on the right. Clicking on a region will move the "
" browser's window to that region."
"
\n"
" - sort genes: Opens the Gene Sorter with a filter to "
" display only those genes in regions that are above the "
" significance threshold. If the graph was uploaded using"
" markers, then a custom Gene Sorter column with the same name as the "
" graph will be created. This column will list all markers for each "
" gene that contain values above the significance threshold."
"
\n"
"
\n");
}