plot


SYNOPSIS

plot  type={RECALC_VS_EXP | PRED_VS_EXP | EXT_PRED_VS_EXP [residuals={YES | NO}; defaults to NO]  \
    | PLS_X_VS_Y [pc=<number of PCs to be used; defaults to the number extracted building the PLS model>]  \
    [y_var_list=<comma/hyphen separated list | ALL; defaults to ALL>]  \
    [labels={NUMBER | ID | NAME | NONE}; defaults to NONE]  \
    | SDEC | R2 | SDEP | Q2  \
    | SCRAMBLED_Q2_VS_R2 | SCRAMBLED_SECV_VS_R2  \
    | PLS_LOADINGS | PLS_WEIGHTS | PLS_SCORES | PCA_LOADINGS | PCA_SCORES  \
    [pc_x=<PC to be plotted on the x axis; defaults to 1>]  \
    [pc_y=<PC to be plotted on the y axis; defaults to 2>]  \
    [pc_z=<PC to be plotted on the z axis>]}  \
    file=<name of the generated files>


DESCRIPTION

The plot keyword is used to generate text files which can be easily converted into 2D and 3D plots for visualization in 3rd party programs. In particular, in addition to a text file with numeric data which can be plotted by means of a spreadsheet, a script for immediate visualization in gnuplot is generated. Both files have the same basename, which can be chosen through the file parameter, while the extension is different (.txt for the text file, .gnuplot for the gnuplot script). Please note that the filename entered through the file parameter should not carry any extension, while it can include the file path. If the gnuplot executable is in the path, it will be launched automatically to visualize the plot if Open3DQSAR is running interactively; as a default, it will be invoked as gnuplot on Linux, Solaris, FreeBSD and Mac OS X, while on Windows wgnuplot.exe will be searched. If the gnuplot executable is not in the path, full path to it (e.g., /usr/local/bin/gnuplot or C:\Program Files\gnuplot\bin\wgnuplot.exe) can be assigned to the O3_GNUPLOT environment variable. The same effect can be obtained setting appropriately the gnuplot variable through the env keyword. Setting explicitly O3_GNUPLOT to a valid path or to "" respectively forces execution or non-execution of gnuplot no matter if Open3DQSAR is running interactively or not.
In the following a brief description of the different types of plot is reported.

All of these four plot types support a number of additional options. The residuals parameter allows to specify whether residuals with respect to real values or predictions should plotted. The label parameter controls whether the object number, the object ID, the object name, or none of them should be added near each data point. The y_var_list option allows to choose whether to write a plot file for each of the dependent variables present in the model or only for a selection of them.

EXAMPLES

# the following command generates a calculated-vs-experimental Y's plot using a previously generated PLS model in which at least 5 principal components had been extracted; namely, a file called plot_name.dat is generated with 2 columns, one for calculated and one for experimental data. Additionally a script called plot_name.gnuplot is generated, ready to be loaded into Gnuplot for visualization
plot  pc=5  type=RECALC_VS_EXP  file=plot_name

# the following command generates a SDEP-vs-PC plot using a previously generated CV model in which at least 4 principal components had been extracted
plot  pc=4  type=SDEP  file=plot_name

# the following command generates a PLS_LOADINGS 2D chart plotting on the x and y axes the first two principal components, respectively
plot  pc_x=1  pc_y=2  type=PLS_LOADINGS  file=plot_name

# the following command generates a PLS_WEIGHTS 3D chart plotting on the x, y, z axes the first three principal components, respectively
plot  pc_x=1  pc_y=2  pc_z=3  type=PLS_WEIGHTS  file=plot_name

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Last update:
May 31. 2015 20:39:42

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