added sort to heatmap to put shared otus at the top and updated some error checking

[mothur.git] / helpcommand.cpp

diff --git a/helpcommand.cpp b/helpcommand.cpp
index e04f63606f05626ceaa7d2e8600dae669c15b845..cb8785acd54ded4493230cddcb364509b2d92d97 100644 (file)
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -39,7 +39,7 @@ int HelpCommand::execute(){
        }else if (globaldata->helpRequest == "read.otu") {
                cout << "The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, " << "\n";
                cout << "collect.shared, rarefaction.shared or summary.shared command.   Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command " << "\n";
-               cout << "or you may use your own. The read.otu command parameter options are list, rabund, sabund, group, order, line and label." << "\n";
+               cout << "or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, line and label." << "\n";
                cout << "The read.otu command can be used in two ways.  The first is to read a list, rabund or sabund and run the collect.single, rarefaction.single or summary.single." << "\n";
                cout << "For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels)." << "\n";
                cout << "The list, rabund or sabund parameter is required, but you may only use one of them." << "\n";
@@ -106,7 +106,6 @@ int HelpCommand::execute(){
                cout << "The get.line command should be in the following format: " << "\n";
                cout << "get.line()" << "\n";
                cout << "Example get.line()." << "\n";
-               cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
        }else if (globaldata->helpRequest == "rarefaction.single") {
                cout << "The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION." << "\n";
                cout << "The rarefaction.single command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster." << "\n";
@@ -187,6 +186,16 @@ int HelpCommand::execute(){
                cout << "The default value for groups is all the groups in your groupfile, iters is 10000, cutoff is 1.0, form is integral and step is 0.01." << "\n";
                cout << "The libshuff command output two files: .coverage and .slsummary their descriptions are in the manual." << "\n";
                cout << "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e.yourIters)." << "\n" << "\n";
+       }else if (globaldata->helpRequest == "heatmap") { 
+               cout << "The heatmap command can only be executed after a successful read.otu command." << "\n";
+               cout << "The heatmap command parameters are groups, line and label.  No parameters are required, but you may not use line and label at the same time." << "\n";
+               cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap." << "\n";
+               cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like a heatmap created for, and are also separated by dashes." << "\n";
+               cout << "The heatmap command should be in the following format: heatmap(groups=yourGroups, line=yourLines, label=yourLabels)." << "\n";
+               cout << "Example heatmap(groups=A-B-C, line=1-3-5)." << "\n";
+               cout << "The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used." << "\n";
+               cout << "The heatmap command outputs a .svg file for each line or label you specify." << "\n";
+               cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
        }else if (globaldata->helpRequest == "quit") {
                cout << "The quit command will terminate Dotur and should be in the following format: " << "\n";
                cout << "quit()" << "\n" << "\n";