added help for heatmap.sim

[mothur.git] / helpcommand.cpp

diff --git a/helpcommand.cpp b/helpcommand.cpp
index 00cd8ddf5a0b089f39f3a8d5d987d59ab204b333..acc53532dac7b21fe274c1f4aabe552a37214542 100644 (file)
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -241,6 +241,18 @@ int HelpCommand::execute(){
                cout << "The default value for scale is log10; your other options are log2 and linear." << "\n";
                cout << "The heatmap.bin 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 == "heatmap.sim") { 
+               cout << "The heatmap.sim command can only be executed after a successful read.otu command." << "\n";
+               cout << "The heatmap.sim command parameters are groups, calc, 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.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, line=yourLines, label=yourLabels)." << "\n";
+               cout << "Example heatmap.sim(groups=A-B-C, line=1-3-5, calc=jabund)." << "\n";
+               cout << "The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used." << "\n";
+               validCalcs->printCalc("heat", cout);
+               cout << "The default value for calc is jclass-thetayc." << "\n";
+               cout << "The heatmap.sim command outputs a .svg file for each calculator you choose at 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 == "venn") { 
                cout << "The venn command can only be executed after a successful read.otu command." << "\n";
                cout << "The venn command parameters are groups, calc, line and label.  No parameters are required, but you may not use line and label at the same time." << "\n";