vtools_report plot_association generates QQ plot and Manhattan plot of p-values from output of vtools associate command. The graphics are powered by the R package ggplot2. Fonts, color, page layout etc can be specified from the command interface, generating high quality and customized graphs.
vtools associate command typically generates two types of output: output of gene based association tests and single variant analysis.
#refGene_name2 sample_size_SBurdenTest statistic_SBurdenTest pvalue_SBurdenTest
AAGAB 1246 14 0.709392
ABHD2 1246 1 0.423756
ACAN 1246 107 0.0235792
ACSBG1 1246 23 0.887873
ACTC1 1246 0 1
ADAL 1246 2 1
ADAMTS17 1246 19 0.875558
ADAM10 1246 0 0.0766778
AGBL1 1246 120 0.119562
...
#chr pos sample_size_SNV beta_x_SNV pvalue_SNV
1 802398 120 0.164128 0.205794
1 861292 316 -0.0339594 0.556444
1 865580 252 0.448666 0.271728
1 866422 316 -0.106212 0.734266
1 865584 268 0.0681559 0.267732
1 865625 303 -0.54794 0.837163
1 866517 311 0.154219 0.17982
1 865662 303 -0.571153 0.881119
1 871129 315 0.0691795 0.476523
Note that
pvalue_ and suffixed by some non-empty character string which will be used as legend names% vtools_report plot_association -h
usage: vtools_report plot_association [-h] [-v {0,1,2}]
{qq,manhattan,manhattan_plain} ...
positional arguments:
{qq,manhattan,manhattan_plain}
qq QQ plot via ggplot2
manhattan Manhattan plot via ggplot2
manhattan_plain Manhattan plot implementation not using ggplot2
optional arguments:
-h, --help show this help message and exit
-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.
% vtools_report plot_association qq -h
usage: vtools_report plot_association qq [-h] [--shape INTEGER]
[--fixed_shape] [--no_slope]
[-t TITLE]
[--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}]
[--width_height INCHES INCHES] [-s]
[-o FILE] [-b]
[-l POSITION [POSITION ...]]
[--label_top INTEGER]
[--label_these NAME [NAME ...]]
[-f SIZE]
optional arguments:
-h, --help show this help message and exit
--shape INTEGER Choose a shape theme (integer 1 to 16) for dots on QQ
plot. Default set to 1.
--fixed_shape Use the same dot-shape theme for all plots
--no_slope Do not plot the diagonal line
graph properties:
-t TITLE, --title TITLE
Title of plot.
--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}
Choose a color theme from the list above to apply to
the plot. (via the 'RColorBrewer' package:
cran.r-project.org/web/packages/RColorBrewer)
--width_height INCHES INCHES
The width and height of the graphics region in inches
-s, --same_page Plot multiple groups of p-values on the same graph
-o FILE, --output FILE
Specify output graph filename. Output is in pdf
format. It can be converted to jpg format via the
'convert' command in Linux (e.g., convert -density 180
p.pdf p.jpg)
variants/genes highlighting:
-b, --bonferroni Plot the horizontal line at 0.05/N on Y-axis
(significance level after Bonferroni correction)
-l POSITION [POSITION ...], --hlines POSITION [POSITION ...]
Additional horizontal line(s) to be drawn on the
Y-axis.
--label_top INTEGER Specify how many top hits (smallest p-values by rank)
you want to highlight with their identifiers in text.
--label_these NAME [NAME ...]
Specify the names of variants (chr:pos, e.g., 1:87463)
or genes (genename, e.g., IKBKB) you want to highlight
with their identifiers in text.
-f SIZE, --font_size SIZE
Font size of text labels. Default set to '2.5'.
% vtools_report plot_association manhattan -h
usage: vtools_report plot_association manhattan [-h]
[--chrom CHROMOSOME [CHROMOSOME ...]]
[--chrom_prefix PREFIX]
[--gene_map FILE] [-t TITLE]
[--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}]
[--width_height INCHES INCHES]
[-s] [-o FILE] [-b]
[-l POSITION [POSITION ...]]
[--label_top INTEGER]
[--label_these NAME [NAME ...]]
[-f SIZE]
optional arguments:
-h, --help show this help message and exit
--chrom CHROMOSOME [CHROMOSOME ...]
Specify the particular chromosome(s) to display. Can
be one or multiple in this list: "1 2 3 4 5 6 7 8 9 10
11 12 13 14 15 16 17 18 19 20 21 22 X Y Un ?:?".
Slicing syntax "?:?" is supported. For example "1:22"
is equivalent to displaying all autosomes; "1:Y" is
equivalent to displaying all mapped chromosomes.
Default set to all including unmapped chromosomes.
--chrom_prefix PREFIX
Prefix chromosome ID with a string. Default is set to
"chr" (X-axis will be displayed as "chr1", "chr2",
etc). Use "None" for no prefix.
--gene_map FILE If the plot units are genes and the program fails to
map certain genes to chromosomes, you can fix it by
providing a text file of genomic coordinate
information of these genes. Each gene in the file is a
line of 3 columns specifying "GENENAME CHROM
MIDPOINT_POSITION", e.g., "IKBKB 8 42128820".
graph properties:
-t TITLE, --title TITLE
Title of plot.
--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}
Choose a color theme from the list above to apply to
the plot. (via the 'RColorBrewer' package:
cran.r-project.org/web/packages/RColorBrewer)
--width_height INCHES INCHES
The width and height of the graphics region in inches
-s, --same_page Plot multiple groups of p-values on the same graph
-o FILE, --output FILE
Specify output graph filename. Output is in pdf
format. It can be converted to jpg format via the
'convert' command in Linux (e.g., convert -density 180
p.pdf p.jpg)
variants/genes highlighting:
-b, --bonferroni Plot the horizontal line at 0.05/N on Y-axis
(significance level after Bonferroni correction)
-l POSITION [POSITION ...], --hlines POSITION [POSITION ...]
Additional horizontal line(s) to be drawn on the
Y-axis.
--label_top INTEGER Specify how many top hits (smallest p-values by rank)
you want to highlight with their identifiers in text.
--label_these NAME [NAME ...]
Specify the names of variants (chr:pos, e.g., 1:87463)
or genes (genename, e.g., IKBKB) you want to highlight
with their identifiers in text.
-f SIZE, --font_size SIZE
Font size of text labels. Default set to '2.5'.
% vtools_report plot_association manhattan_plain -h
usage: vtools_report plot_association manhattan_plain [-h]
[--chrom CHROMOSOME [CHROMOSOME ...]]
[--chrom_prefix PREFIX]
[--gene_map FILE]
[-t TITLE]
[--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}]
[--width_height INCHES INCHES]
[-s] [-o FILE] [-b]
[-l POSITION [POSITION ...]]
[--label_top INTEGER]
[--label_these NAME [NAME ...]]
[-f SIZE]
optional arguments:
-h, --help show this help message and exit
--chrom CHROMOSOME [CHROMOSOME ...]
Specify the particular chromosome(s) to display. Can
be one or multiple in this list: "1 2 3 4 5 6 7 8 9 10
11 12 13 14 15 16 17 18 19 20 21 22 X Y Un ?:?".
Slicing syntax "?:?" is supported. For example "1:22"
is equivalent to displaying all autosomes; "1:Y" is
equivalent to displaying all mapped chromosomes.
Default set to all including unmapped chromosomes.
--chrom_prefix PREFIX
Prefix chromosome ID with a string. Default is set to
"chr" (X-axis will be displayed as "chr1", "chr2",
etc). Use "None" for no prefix.
--gene_map FILE If the plot units are genes and the program fails to
map certain genes to chromosomes, you can fix it by
providing a text file of genomic coordinate
information of these genes. Each gene in the file is a
line of 3 columns specifying "GENENAME CHROM
MIDPOINT_POSITION", e.g., "IKBKB 8 42128820".
graph properties:
-t TITLE, --title TITLE
Title of plot.
--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}
Choose a color theme from the list above to apply to
the plot. (via the 'RColorBrewer' package:
cran.r-project.org/web/packages/RColorBrewer)
--width_height INCHES INCHES
The width and height of the graphics region in inches
-s, --same_page Plot multiple groups of p-values on the same graph
-o FILE, --output FILE
Specify output graph filename. Output is in pdf
format. It can be converted to jpg format via the
'convert' command in Linux (e.g., convert -density 180
p.pdf p.jpg)
variants/genes highlighting:
-b, --bonferroni Plot the horizontal line at 0.05/N on Y-axis
(significance level after Bonferroni correction)
-l POSITION [POSITION ...], --hlines POSITION [POSITION ...]
Additional horizontal line(s) to be drawn on the
Y-axis.
--label_top INTEGER Specify how many top hits (smallest p-values by rank)
you want to highlight with their identifiers in text.
--label_these NAME [NAME ...]
Specify the names of variants (chr:pos, e.g., 1:87463)
or genes (genename, e.g., IKBKB) you want to highlight
with their identifiers in text.
-f SIZE, --font_size SIZE
Font size of text labels. Default set to '2.5'.
zcat genetest.result.gz | vtools_report plot_association qq -o genes_qq1
zcat genetest.result.gz | vtools_report plot_association qq -s --color Dark2 -b -o genes_qq\
2
zcat genetest.result.gz | vtools_report plot_association qq -t "Demo QQ plot" -b -o genes_q\
q3
zcat genetest.result.gz | vtools_report plot_association qq -t "Demo otherwise shaped QQ pl\
ot" -s -b --shape 12 -o genes_qq4
zcat varianttest.result.gz | vtools_report plot_association qq -o variants_qq1
zcat varianttest.result.gz | vtools_report plot_association qq -s --color Dark2 -b -o varia\
nts_qq2
zcat varianttest.result.gz | vtools_report plot_association qq -t "Demo QQ plot" -b -o vari\
ants_qq3
zcat varianttest.result.gz | vtools_report plot_association qq -t "Demo otherwise shaped QQ\
plot" -s -b --shape 12 -o variants_qq4
zcat genetest.result.gz | vtools_report plot_association manhattan -t "Demo Manhattan plot"\
--color Dark2 --s -b -o genes_man1
zcat genetest.result.gz | vtools_report plot_association manhattan -t "Demo Manhattan plot"\
--chrom 1:22 --chrom_prefix None --same_page -o genes_man2
zcat genetest.result.gz | vtools_report plot_association manhattan_plain -t "Demo Manhattan\
plain plot" --color Dark2 --s -b -o genes_man3
zcat genetest.result.gz | vtools_report plot_association manhattan_plain -t "Demo Manhattan\
plain plot" --chrom 1:22 --chrom_prefix None --same_page -o genes_man4
zcat varianttest.result.gz | vtools_report plot_association manhattan -t "Demo Manhattan pl\
ot" --color Dark2 --s -b -o variants_man1
zcat varianttest.result.gz | vtools_report plot_association manhattan -t "Demo Manhattan pl\
ot" --chrom 1:22 --chrom_prefix None --same_page -o variants_man2
zcat varianttest.result.gz | vtools_report plot_association manhattan_plain -t "Demo Manhat\
tan plain plot" --color Dark2 --s -b -o variants_man3
zcat varianttest.result.gz | vtools_report plot_association manhattan_plain -t "Demo Manhat\
tan plain plot" --chrom 1:22 --chrom_prefix None --same_page -o variants_man4