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Merge pull request #12 from gtrichard/dsBedFeaturesDensity
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dsBedFeaturesDensity
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gtrichard authored Feb 14, 2020
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13 changes: 7 additions & 6 deletions README.md
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Expand Up @@ -7,7 +7,7 @@ https://anaconda.org/bioconda/deepstats/badges/license.svg)

**deepStats 0.3.1 is a statistical and dataviz toolbox for deeptools, genomic signals, and more (GOterms, etc).**

It aims at providing statistical analyses and streamlining the production of high quality, color-blind friendly, and fully customisable plots (up to the fonts!) for your classic genomic datasets (.bed, .bigwig, gene lists). The goal of deepStats is thus to significantly decrease the amount of time spent in Inkscape/Illustrator to get publication ready plots, and decreasing the research time allotted to finding proper statistical analyses for your genomic signals and datasets.
It aims at providing statistical analyses and streamlining the production of high quality, color-blind friendly, and fully customisable plots (up to the fonts!) for your classic genomic datasets (.bed, .bigwig, gene lists). The goal of deepStats is thus to significantly decrease the amount of time spent in Inkscape/Illustrator to get publication ready plots, and decreasing the research time allotted to finding proper statistical analyses for your genomic signals and datasets. It also aims at giving tools to complement deepTools functions.

**This is currently a Work In Progress**

Expand All @@ -18,10 +18,13 @@ https://github.com/gtrichard/deepStats/wiki

| Tool name | Description |
| ----------------- | ---------------------------------------------------- |
| [dsCompareCurves] | compares multiple genomic scores at multiple regions sets by bootstraps and per-bin distribution test |
| [dsCompareCurves] | compares multiple genomic scores at multiple regions sets by bootstraps and per-bin distribution test. |
| [dsComputeBEDDensity] | computes BED files features density along the genome given a bin size, output as bedGraphs. |
| [dsComputeGCCoverage] | calculates the GC% along the genome for bins of a given size in a memory efficient way. |

[dsCompareCurves]: https://github.com/gtrichard/deepStats/wiki/dsCompareCurves

[dsComputeBEDDensity]: https://github.com/gtrichard/deepStats/wiki/dsComputeBEDDensity
[dsComputeGCCoverage]: https://github.com/gtrichard/deepStats/wiki/dsComputeGCCoverage

## Citation

Expand All @@ -41,7 +44,7 @@ conda activate deepStats

- **As R Notebooks**

Currently, R notebooks are not up-to-date.
**Currently, R notebooks are not up-to-date.**

Install the following packages in your R environment:
```
Expand All @@ -62,5 +65,3 @@ git clone https://github.com/gtrichard/deepStats
- **As Galaxy wrappers**

You can install deepStats in a Galaxy instance through the [Galaxy Tool Shed](https://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=name&operation=view_or_manage_repository&f-free-text-search=deepstats&id=4125c47ee1118a75)


136 changes: 58 additions & 78 deletions bin/dsCompareCurves
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#!/usr/bin/env Rscript

suppressMessages( library( 'optparse' ) )
# BOOTSTRAPS ON DEEPTOOLS COMPUTE MATRIX OUTPUT AND PLOT
suppressMessages( library( 'argparse' ) )
suppressMessages( library( 'boot' ) )
suppressMessages( library( 'ggplot2' ) )
suppressMessages( library( 'cowplot' ) )
Expand All @@ -15,103 +15,83 @@ options( show.error.locations = TRUE )

#### ARGUMENTS ####

option_list = list(
parser <- ArgumentParser(description= "dsCompareCurves assesses if multiple genomics signals ( ChIP-seq, ATAC-seq... ) are significantly different or not between conditions ( control, KO1, KO2, etc ). `dsCompareCurves` uses bootstraps and corrected Wilcoxon Rank-sum tests to do so. The input of this tool corresponds to the output of deepTools `computeMatrix --outFileNameMatrix`. If multiple region sets have been used in deepTools, one plot and tab-delimited table will be produced for each set of regions.",
usage = "dsCompareCurves --input file.txt --output results")

make_option( c( "-i","--input" ), type="character", default=NULL,
help="DeepTools file obtained from computeMatrix --outFileNameMatrix.
Alternatively, a .dscc file from previous dsCompareCurves runs can be provided
for replotting purposes and to avoid the bootstraps computation once more.", metavar="character" ),
parser$add_argument("--input","-i", type="character", default=NULL,
help="DeepTools file obtained from computeMatrix --outFileNameMatrix. Alternatively, a .dscc file from previous dsCompareCurves runs can be provided for replotting purposes and to avoid the bootstraps computation once more.", metavar="character" )

make_option( c( "--output", "-o" ), type="character", default=NULL,
help="Output prefix. Three files will be generated, a .pdf file containing the plot
and a .dscc file containing the bootsraps information ( RDS file ). If a .dscc file
is provided as input, only the plot will be produced as pdf.", metavar="character" ),
parser$add_argument("--output", "-o", type="character", default=NULL,
help="Output prefix. Three files will be generated, a .pdf file containing the plot and a .dscc file containing the bootsraps information ( RDS file ). If a .dscc file is provided as input, only the plot will be produced as pdf.", metavar="character" )

make_option( c( "--comparison", "-c" ), type="character", default=NULL,
help="When specifying 'regions' or 'scores', force a given comparison. The correct comparison to
perform is otherwise automatically detected.", metavar="character" ),
parser$add_argument("--comparison", "-c", type="character", default=NULL,
help="When specifying 'regions' or 'scores', force a given comparison. The correct comparison to perform is otherwise automatically detected.", metavar="character" )

make_option( c( "--scoreLabels" ), type="character", default=NULL,
help="Names of the scores to be displayed on the plots. It must be provided as text seperated by semi-colons, i.e.
'Score A;Score B;Score C'.", metavar="character" ),
# nargs = '+' should be used at some point, bug changing this would break galaxy and the documentation and would require "" for each label.
parser$add_argument("--scoreLabels", type="character", default=NULL,
help="Names of the scores to be displayed on the plots. It must be provided as text seperated by semi-colons, i.e. 'Score A;Score B;Score C'.", metavar="character" )

make_option( c( "--regionLabels" ), type="character", default=NULL,
help="Names of the regions to be displayed on the plots. It must be provided as text seperated by semi-colons, i.e.
'Regions A; Regions B; Regions C'.", metavar="character" ),
parser$add_argument("--regionLabels", type="character", default=NULL,
help="Names of the regions to be displayed on the plots. It must be provided as text seperated by semi-colons, i.e. 'Regions A; Regions B; Regions C'.", metavar="character" )

make_option( c( "--signalName" ), type="character", default="Genomic signal",
help="Name given to the signal, for instance 'H3K4me3 log2input'.
Default: 'Genomic signal'", metavar="character" ),
parser$add_argument("--signalName", type="character", default="Genomic signal",
help="Name given to the signal, for instance 'H3K4me3 log2input'. Default: 'Genomic signal'", metavar="character" )

make_option( c( "--bootstraps", "-b" ), type="integer", default=1000,
help="Number of bootstraps to perform. Default: 1000.", metavar="integer" ),
parser$add_argument("--bootstraps", "-b", type="integer", default=1000,
help="Number of bootstraps to perform. Default: 1000.", metavar="integer" )

make_option( c( "--bootstrapsCI" ), type="numeric", default=0.95,
help="Confidence intervals (CI) threshold for bootstraps. Default: 0.95.", metavar="numeric" ),
parser$add_argument("--bootstrapsCI", type="double", default=0.95,
help="Confidence intervals (CI) threshold for bootstraps. Default: 0.95.", metavar="numeric" )

make_option( c( "--CPU", "-p" ), type="integer", default=4,
help="Number of CPU to use. Default: 4.", metavar="integer" ),
parser$add_argument("--CPU", "-p", type="integer", default=4,
help="Number of CPU to use. Default: 4.", metavar="integer" )

# make_option( c( "--wilcoxStartBin" ), type="numeric", default=NULL,
# parser$add_argument("--wilcoxStartBin", type="numeric", default=NULL,
# help="The start bin number used to restrict the corrected
# wilcoxon test to a given portion of the plot. An integer must be provided.
# Default: first bin.", metavar="numeric" ),
# Default: first bin.", metavar="numeric" )

# make_option( c( "--wilcoxEndBin" ), type="numeric", default=NULL,
# parser$add_argument("--wilcoxEndBin", type="numeric", default=NULL,
# help="The end bin number used to restrict the corrected
# wilcoxon test to a given portion of the plot. An integer must be provided.
# Default: last bin.", metavar="numeric" ),
# Default: last bin.", metavar="numeric" )

parser$add_argument("--wilcoxThreshold", type="double", default=0.05,
help="Threshold used to define significant bins on the Wilcoxon rank-sum test plot. Default: 0.05", metavar="numeric" )

make_option( c( "--wilcoxThreshold" ), type="numeric", default=0.05,
help="Threshold used to define significant bins on the Wilcoxon rank-sum
test plot. Default: 0.05", metavar="numeric" ),
parser$add_argument("--firstRegionName", type="character", default="TSS",
help="Name of the central or left region. Default: TSS", metavar="character" )

make_option( c( "--firstRegionName" ), type="character", default="TSS",
help="Name of the central or left region. Default: TSS", metavar="character" ),
parser$add_argument("--secondRegionName", type="character", default="TES",
help="Name of the right region, only used when deeptools computeMatrix ran in scaled-regions mode. Default: TES", metavar="character" )

make_option( c( "--secondRegionName" ), type="character", default="TES",
help="Name of the right region, only used when deeptools computeMatrix
ran in scaled-regions mode. Default: TES", metavar="character" ),
parser$add_argument("--bootPlotShareY", type="character", default="TRUE",
help="Given TRUE or FALSE, defines if the bootstraps plots should share the same scale on the y axis or not. Default: TRUE", metavar="character" )

make_option( c( "--bootPlotShareY" ), type="character", default="TRUE",
help="Given TRUE or FALSE, defines if the bootstraps plots should
share the same scale on the y axis or not. Default: TRUE", metavar="character" ),
parser$add_argument("--bootPlotColors", type="character", default=NULL,
help="Change the bootstraps plot color palette to a user-provided one. The file must be tab-delimited and contain for each line two HTML color codes ( #3366CC #769EF2 ). The first column corresponds to the mean color, the second column corresponds to the color of the bootstrap confidence interval shadowed area. The default color scale contains 6 colors that are color blind friendly using the dichromat R package.", metavar="character" )

make_option( c( "--bootPlotColors" ), type="character", default=NULL,
help="Change the bootstraps plot color palette to a user-provided one. The file must
be tab-delimited and contain for each line two HTML color codes ( #3366CC #769EF2 ).
The first column corresponds to the mean color, the second column corresponds to the
color of the bootstrap confidence interval shadowed area. The default color scale
contains 6 colors that are color blind friendly using the dichromat R package.", metavar="character" ),
parser$add_argument("--bootPlotRatio", type="double", default=0.85,
help="Changes the aspect ratio of the plot. A value < 1 results in a wide plot, a value > 1 results in a narrow plot. Default: 0.85.", metavar="numeric" )

make_option( c( "--bootPlotRatio" ), type="character", default=0.85,
help="Changes the aspect ratio of the plot. A value < 1 results in a wide plot,
a value > 1 results in a narrow plot. Default: 0.85.", metavar="character" ),
parser$add_argument("--bootPlotWidth", type="double", default=5.2,
help="How large the bootstraps plot should be. Default: 5.2", metavar="numeric" )

make_option( c( "--bootPlotWidth" ), type="numeric", default=5.2,
help="How large the bootstraps plot should be. Default: 5.2", metavar="numeric" ),
parser$add_argument("--bootPlotHeight", type="double", default=3.7,
help="How tall the bootstraps plot should be. Default: 3.7", metavar="numeric" )

make_option( c( "--bootPlotHeight" ), type="numeric", default=3.7,
help="How tall the bootstraps plot should be. Default: 3.7", metavar="numeric" ),
parser$add_argument("--wilcoxPlotWidth", type="double", default=4.6,
help="How large the Wilcoxon rank-sum test plot should be. Default: 4.6", metavar="numeric" )

make_option( c( "--wilcoxPlotWidth" ), type="numeric", default=4.6,
help="How large the Wilcoxon rank-sum test plot should be. Default: 4.6", metavar="numeric" ),
parser$add_argument("--wilcoxPlotHeight", type="double", default=4.6,
help="How tall the Wilcoxon rank-sum test plot should be. Default: 4.6", metavar="numeric" )

make_option( c( "--wilcoxPlotHeight" ), type="numeric", default=4.6,
help="How tall the Wilcoxon rank-sum test plot should be. Default: 4.6", metavar="numeric" ),
parser$add_argument("--font", type="character", default=NULL,
help="Font used for plotting, given a TTF file. Default is usually Helvetica.", metavar="character" )

make_option( c( "--font" ), type="character", default=NULL,
help="Font used for plotting, given a TTF file. Default is usually Helvetica.", metavar="character" )
);
opt <- parser$parse_args()

opt_parser = OptionParser( description= "
dsCompareCurves 0.3.1 assesses if multiple genomics signals ( ChIP-seq, ATAC-seq... ) are significantly different or
not between conditions ( control, KO1, KO2, etc ). `dsCompareCurves` uses bootstraps and corrected
Wilcoxon Rank-sum tests to do so. The input of this tool corresponds to the output of deepTools
`computeMatrix --outFileNameMatrix`. If multiple region sets have been used in deepTools, one plot and
tab-delimited table will be produced for each set of regions.",
usage = "dsCompareCurves --input file.txt --output results", option_list=option_list );
opt = parse_args( opt_parser );
#### SANITY CHECK ####

if ( is.null( opt$input ) ) {
print_help( opt_parser )
Expand Down Expand Up @@ -140,13 +120,13 @@ setwd( normalizePath( dirname( opt$output ) ) )

#### REMOVE BAD LABELS ####

if ( opt$scoreLabels=="" ) {
opt$scoreLabels <- NULL
}
#if ( opt$scoreLabels== NULL ) {
# opt$scoreLabels <- NULL
#}

if ( opt$regionLabels=="" ) {
opt$regionLabels <- NULL
}
#if ( opt$regionLabels=="" ) {
# opt$regionLabels <- NULL
#}

#### METADATA EXTRACTION ####

Expand Down
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