started shared utilities, updates to venn and heatmap added tree.groups command

[mothur.git] / helpcommand.cpp

diff --git a/helpcommand.cpp b/helpcommand.cpp
index 05aaff0b0d58a46b380223b5b52ed84812e38c57..7ac616feb6cc82be610c73a7e853d50a17693998 100644 (file)
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -194,14 +194,16 @@ int HelpCommand::execute(){
                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, sorted, line and label.  No parameters are required, but you may not use line and label at the same time." << "\n";
+               cout << "The heatmap command parameters are groups, sorted, scaler, 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 sorted parameter allows you to choose to see the file with the shared otus at the top or the exact representation of your input file. " << "\n";
+               cout << "The sorted parameter allows you to choose to see the file with the shared otus at the top or the otus in the order they appear in your input file. " << "\n";
+               cout << "The scaler parameter allows you to choose the range of color your bin information will be displayed with." << "\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, sorted=yourSorted, line=yourLines, label=yourLabels)." << "\n";
-               cout << "Example heatmap(groups=A-B-C, line=1-3-5, sorted=0)." << "\n";
+               cout << "Example heatmap(groups=A-B-C, line=1-3-5, sorted=0, scaler=log10)." << "\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 default value for sorted is 1 meaning you want the shared otus on top, you may change it to 0 meaning the exact representation of your input file." << "\n";
+               cout << "The default value for scaler is log2; your other options are log10 and linear." << "\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 == "venn") { 
@@ -213,6 +215,8 @@ int HelpCommand::execute(){
                cout << "Example venn(groups=A-B-C, line=1-3-5, calc=sharedsobs-sharedchao)." << "\n";
                cout << "The default value for groups is all the groups in your groupfile up to 4, and all lines in your inputfile will be used." << "\n";
                cout << "The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups." << "\n";
+               cout << "The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a list and group file or a shared file." << "\n";
+               cout << "The only estmiator available four 4 groups is sharedsobs." << "\n";
                cout << "The venn command outputs a .svg file for each calculator you specify at each distance you choose." << "\n";
                cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
        }else if (globaldata->helpRequest == "bin.seqs") {