Plots

--plot

_images/all.jpg

This argument allows to plot several types of plots, as desribed bellow.

Note

For using --plot when working on a remote server (e.g., via SSH), make sure X11-forwarding is enabled.

Note

The example commands described bellow assume that the user generated GLINT files with covariates file and phenotypes file.

Note

For each plot generated by GLINT two identical figures are saved in two different formats: .png file and .eps file. The latter is a publication quality figure.

Note

Use --out in order to change the default output name.



Outliers detection

--plotpcs

Generates scatter plots for visualizing the couples of principal components (PCs) of the data. The generated plots help in detecting outliers visualy by marking a grid of standard deviations. This plot can guide the selection of values for the --maxpcstd argument.

For example:

python glint.py --datafile datafile.glint --plot --plotpcs

will generate a figure titled pcs_plot.png with scatter plots of the first couple of PCs of the data (you can change the number of PCs couples to plot with the --numpcs flag as described below).

--numpcs

Allows to select the number of PCs to plot when using the --plotpcs argument (default is 2).

For example:

python glint.py --datafile datafile.glint --plot --plotpcs --numpcs 3

will plot scatter plots of the first 3 PCs of the data



Visualize EWAS results

The following arguments allow to generate plots based on result files generated using the --ewas argument.

Note

The --plot argument can be used together with --ewas in order to run EWAS and plot the results in a single command. More than one plot can be selected.

--qqplot

Generates a qq-plot from a results file generated by running --ewas.

For example:

python glint.py --datafile datafile.glint --plot --qqplot results.glint.linreg.txt

will generate a qq-plot from the results in the results.glint.linreg.txt file.

Alternatively, run directly with EWAS:

python glint.py --datafile datafile.glint --ewas --linreg --plot --qqplot

--manhattan

Generates a Manhattan plot from a results file generated by running --ewas.

For example:

python glint.py --datafile datafile.glint --plot --manhattan results.glint.linreg.txt

will generate Manhattan plot from the results in the results.glint.linreg.txt file.

Alternatively, run directly with EWAS:

python glint.py --datafile datafile.glint --ewas --linreg --plot --manhattan