% vtools_report plot_pheno_fields -h
usage: vtools_report plot_pheno_fields [-h]
[--samples [SAMPLES [SAMPLES ...]]]
[--save_data FILENAME]
[--save_script FILENAME] [--width px]
[--height px] [--hist name]
[--norm_curve] [--dot name]
[--dot_size pt]
[--discrete_color {Dark2,grayscale,default,BrBG,PiYG,PRGn,PuOr,RdBu,RdGy,RdYlBu,RdYlGn,Spectral,Accent,Paired,Pastel1,Pastel2,Set1,Set2,Set3,Blues,BuGn,BuPu,GnBu,Greens,Greys,Oranges,OrRd,PuBu,PuBuGn,PuRd,Purples,RdPu,Reds,YlGn,YlGnBu,YlOrBr,YlOrRd}]
[--box name] [--stratify C [C ...]]
[--outlier_size pt]
[--color {Dark2,grayscale,default,BrBG,PiYG,PRGn,PuOr,RdBu,RdGy,RdYlBu,RdYlGn,Spectral,Accent,Paired,Pastel1,Pastel2,Set1,Set2,Set3,Blues,BuGn,BuPu,GnBu,Greens,Greys,Oranges,OrRd,PuBu,PuBuGn,PuRd,Purples,RdPu,Reds,YlGn,YlGnBu,YlOrBr,YlOrRd}]
[-v {0,1,2}]
fields [fields ...]
positional arguments:
fields A list of fields that will be outputted.
optional arguments:
-h, --help show this help message and exit
--samples [SAMPLES [SAMPLES ...]]
Conditions based on which samples are selected.
Default to all samples.
--save_data FILENAME Save data to file.
--save_script FILENAME
Save R script to file.
--width px Width of plot. Default to 800.
--height px Height of plot. Default to 600.
-v {0,1,2}, --verbosity {0,1,2}
Output error and warning (0), info (1) and debug (2)
information of vtools and vtools_report. Debug
information are always recorded in project and
vtools_report log files.
Draw histogram:
--hist name File name of the outputted figure, which can have type
PDF, EPS, or JPG. Multiple files might be produced if
more than one figure is produced (e.g.
MyFig_$FIELD1.pdf, MyFig_$FILED2.pdf if MyFig.pdf is
specified)
--norm_curve Add a normal distribution N(mean, stdev) density curve
to the histogram.
Draw dot plot. Allow up to 3 input fields: for single input
field, the values will be plotted on y-axis with index being x-axis; for two input fields, the first
field will be plotted on x-axis and the second field on y-axis; for three input fields, values of
the third input field is represented by color of the dots.:
--dot name File name of the outputted figure, which can have type
PDF, EPS, or JPG.
--dot_size pt Size of dots. Default is 2.0
--discrete_color {Dark2,grayscale,default,BrBG,PiYG,PRGn,PuOr,RdBu,RdGy,RdYlBu,RdYlGn,Spectral,Accent,Paired,Pastel1,Pastel2,Set1,Set2,Set3,Blues,BuGn,BuPu,GnBu,Greens,Greys,Oranges,OrRd,PuBu,PuBuGn,PuRd,Purples,RdPu,Reds,YlGn,YlGnBu,YlOrBr,YlOrRd}
If specified, the third field of input will be treated
as "factor" data.
Draw box plot. Allow one or more input fields and produce
box plot for all fields in one graph. With --stratify option, box plot will be generated for field
in different strata, if there is only one input field, or for the first field in different strata of
the second field, if there are two input fields.:
--box name File name of the outputted figure, which can have type
PDF, EPS, or JPG.
--stratify C [C ...] Cutoff values to stratify data in the input field for
box plot. When this option is on, only one input field
is allowed.
--outlier_size pt Size of outlier dots. Default is 2.0
--color {Dark2,grayscale,default,BrBG,PiYG,PRGn,PuOr,RdBu,RdGy,RdYlBu,RdYlGn,Spectral,Accent,Paired,Pastel1,Pastel2,Set1,Set2,Set3,Blues,BuGn,BuPu,GnBu,Greens,Greys,Oranges,OrRd,PuBu,PuBuGn,PuRd,Purples,RdPu,Reds,YlGn,YlGnBu,YlOrBr,YlOrRd}
Color theme for boxes.
File type of graph (pdf, png, eps, etc) are determined by output file name extension. Common graphic options
--save_data and --save_script: save data and script to files. If you want to customize the graph, you can save the data and script, make changes, and run Rscript --slave saved_code.R < saved_data.txt--width and --height: controls the size of the graph generated--color and --discrete_color: choose customized coloring theme for box plot and dot plotThe snapshot vt_plots containing phenotype information of ~1000 samples is used to demonstrate various graphs that can be generated.
% vtools init plot
% vtools admin --load_snapshot vt_plots
% vtools_report plot_pheno_fields BMI logBMI BMI_qnormalized --hist hist.pdf --norm_curve
Plot single field, stratified by given thresholds:
% vtools_report plot_pheno_fields BMI --box box.pdf --stratify 21 23 25 27 29
s
Plot single field, stratified by another field with given thresholds:
% vtools_report plot_pheno_fields BMI gender --box box.pdf --stratify 2
In this example, BMI values are stratified by samples gender information. Gender is 1 (“Below 2.0”) for males, and 2 (“2.0 or more”) for females.
Plot multiple fields on the same graph:
% vtools_report plot_pheno_fields MDS1 MDS2 --box box.pdf --color Accent
Dot plot for single field
% vtools_report plot_pheno_fields BMI --dot dot.pdf
Dot plot for two fields
% vtools_report plot_pheno_fields BMI logBMI --dot dot.pdf
Colored dot plot for three fields, with the third field being a continuous variable
% vtools_report plot_pheno_fields MDS1 MDS2 BMI --dot dot.pdf
Colored dot plot for three fields, with the third field being a discrete variable
% vtools_report plot_pheno_fields MDS1 MDS2 Population --dot dot.pdf --discrete_color Accent