Tool Usage

Category 1: Tests for regions versus regions

Projection Test

Commands:
rgt-viz projection -r <experiment_matrix_ref> -q <experiment_matrix_que> <output_directory> [options]
Required Inputs:
Option Name Type Default Description
<experiment_matrix_ref> File None The experiment matrix should contain all the reference regions for projection test. Check more details on Experiment Matrix Format.
<experiment_matrix_que> File None The experiment matrix should contain all the query regions for projection test. Check more details on Experiment Matrix Format.
<output_directory> String None Define the directory which contains all the results, for example, project name or the date.
Optional Inputs:
Option Name Type Default Description
-h, –help Boolean False If this option is used, it shows the help message and exit.
-t, –title String projection_test Define the title shown on the top of the plot and also the folder name.
-g String None Group the data by any optional column (for example, ‘cell’) of experimental matrix, or None.
-c String regions Color the data by any optional column (for example, ‘cell’) of experimental matrix, or None.
-bg File None Define a BED file as background. If not defined, the background is whole genome according to the given organism.
-union Boolean False Take the union of references as background for binomial test.
-organism String  hg19 Define the organism.
-log Boolean False Set y axis of the plot in log scale.
-color Boolean False Define the specific colors with the given column “color” in experimental matrix. The color should be in the format of matplotlib.colors. For example, “r” for red, “b” for blue, or “(100, 35, 138)” for RGB.
-show Boolean False Show the figure in the screen.
-table Boolean False Store the tables of the figure in text format.
Outputs:

The projection test will generate a directory named “projection_test” by default under the given output directory name. The result files are:

  • projection.html: The webpage displays all the graphics and statistical result.
  • parameters.txt: Record the time, user, commands with given arguments and processing time.
  • projection_test.pdf & projection_test.png: The barplot which displays the ratio of overlaps on each query.

Intersection Test

Commands:
rgt-viz intersect -r <experiment_matrix_ref> -q <experiment_matrix_que> <output_directory> [options]
Required Inputs:
Option Name Type Default Description
<experiment_matrix_ref> File None The experiment matrix should contain all the reference regions for projection test. Check more details on Experiment Matrix Format.
<experiment_matrix_que> File None The experiment matrix should contain all the query regions for projection test. Check more details on Experiment Matrix Format.
<output_directory> String None Define the directory which contains all the results, for example, project name or the date.
Optional inputs:
Option Name Type Default Description
-h, –help Boolean False If this option is used, it shows the help message and exit.
-t, –title String projection_test Define the title shown on the top of the plot and also the folder name.
-g String None Group the data by any optional column (for example, ‘cell’) of experimental matrix, or None.
-c String regions Color the data by any optional column (for example, ‘cell’) of experimental matrix, or None.
-organism String  hg19 Define the organism.
-bg File None Define a BED file as background. If not defined, the background is whole genome according to the given organism.
-m {count,bp} String count Define the mode of calculating intersection. ‘count’ outputs the number of overlapped regions. ‘bp’ outputs the coverage (basepair) of intersection.
-tc Integer None Define the threshold (in percentage) of reference length for intersection counting. For example, ’20’ means that the query which overlaps more than 20% of reference is counted as intersection.
-ex Integer None Define the extension(in percentage) of reference length for intersection counting. For example, ’20’ means that each region of reference is extended by 20% in order to include proximal queries.
-log Boolean False Set y axis of the plot in log scale.
-color Boolean False Define the specific colors with the given column “color” in experimental matrix. The color should be in the format of matplotlib.colors. For example, “r” for red, “b” for blue, or “(100, 35, 138)” for RGB.
-show Boolean False Show the figure in the screen.
-table Boolean False Store the tables of the figure in text format.
-stest Integer 0 Define the repetition time of random subregion test between reference and query.
Outputs:

The intersection test will generate a directory named “intersection_test” by default under the given output directory name. The result files are:

  • intersection.html: The webpage displays all the graphics and statistical result.
  • parameters.txt: Record the time, user, commands with given arguments and processing time.
  • Some graphics in png and pdf format.

Jaccard Test

Commands:
rgt-viz jaccard -r <experiment_matrix_ref> -q <experiment_matrix_que> <output_directory> [options]
Required Inputs:
Option Name Type Default Description
<experiment_matrix_ref> File None The experiment matrix should contain all the reference regions for projection test. Check more details on Experiment Matrix Format.
<experiment_matrix_que> File None The experiment matrix should contain all the query regions for projection test. Check more details on Experiment Matrix Format.
<output_directory> String None Define the directory which contains all the results, for example, project name or the date.
Optional inputs:
Option Name Type Default Description
-h, –help Boolean False If this option is used, it shows the help message and exit.
-t, –title String projection_test Define the title shown on the top of the plot and also the folder name.
-g String None Group the data by any optional column (for example, ‘cell’) of experimental matrix, or None.
-c String regions Color the data by any optional column (for example, ‘cell’) of experimental matrix, or None.
-organism String  hg19 Define the organism.
-rt Integer 500 Define how many times to run the randomization.
-nlog Boolean False Set y axis of the plot not in log scale.
-color Boolean False Define the specific colors with the given column “color” in experimental matrix. The color should be in the format of matplotlib.colors. For example, “r” for red, “b” for blue, or “(100, 35, 138)” for RGB.
-show Boolean False Show the figure in the screen.
-table Boolean False Store the tables of the figure in text format.
Outputs:

The Jaccard test will generate a directory named “jaccard_test” by default under the  given output directory name. The result files are:

  • jaccard.html: The webpage displays all the graphics and statistical result.
  • parameters.txt: Record the time, user, commands with given arguments and processing time.
  • Some graphics in png and pdf format.

Combinatorial Test

in progress…

Category 2: Tests for regions versus signals

Boxplot

Commands:
rgt-viz boxplot <experiment_matrix> -o <output_directory> [options]
Required Inputs:
Option Name Type Default Description
<experiment_matrix> File None The file name of the input Experimental Matrix file. Recommended to add more columns for more information for ploting. For example, cell type or factors. Check more details on Experiment Matrix Format.
<output_directory> String None The directory name for the output files. For example, projectname.
Optional inputs:
Option Name Type Default Description
-h, –help Boolean False If this option is used, it shows the help message and exit.
-t, –title String lineplot Define the title shown on the top of the plot and also the folder name.
-g String reads Group the data by reads (needs ‘factor’ column), regions (needs ‘factor’ column), another name of column (for example, ‘cell’) in the header of experimental matrix, or None. (Default: reads)
-c String regions Color the data by reads (needs ‘factor’ column), regions (needs ‘factor’ column), another name of column (for example, ‘cell’) in the header of experimental matrix, or None. (Default: regions)
-s String  None Sort the data by reads (needs ‘factor’ column), regions (needs ‘factor’ column), another name of column (for example, ‘cell’) in the header of experimental matrix, or None. (Default:None)
-sy Boolean False Share y axis for convenience of comparison.
-nlog Boolean False Set y axis of the plot not in log scale.
-color Boolean False Define the specific colors with the given column “color” in experimental matrix. The color should be in the format of matplotlib.colors. For example, “r” for red, “b” for blue, or “(100, 35, 138)” for RGB.
-nqn Boolean False No quantile normalization in calculation.
-df Boolean False Show the difference of the two signals which share the same labels.The result is the subtraction of the first to the second.
-ylim Float None Define the limit of y axis.
-p Float 0.01 Define the significance level for multiple test. Default: 0.01
-show Boolean False Show the figure in the screen.
-table Boolean False Store the tables of the figure in text format.
Outputs:

In the folder with the given name (-t), you can find the following files:

  • index.html: The webpage displays all the graphics and statistical result.
  • parameters.txt: Record the time, user, commands with given arguments and processing time.
  • Some graphics in png and pdf format.

Lineplot & Heatmap

Commands:
rgt-viz lineplot <experiment_matrix> -o <output_directory> [options]
Required Inputs:
Option Name Type Default Description
<experiment_matrix> File None The file name of the input Experimental Matrix file. Recommended to add more columns for more information for ploting. For example, cell type or factors. Check more details on Experiment Matrix Format.
<output_directory> String None The directory name for the output files. For example, projectname.
Optional inputs:
Option Name Type Default Description
-h, –help Boolean False If this option is used, it shows the help message and exit.
-t, –title String lineplot Define the title shown on the top of the plot and also the folder name.
-center String midpoint Define the center to calculate coverage on the regions. Options are: midpoint, leftend, rightend, bothends, upstream, downstream.(Default: midpoint) The bothend mode will flap the right end region for calculation.
-g String reads Group the data by reads (needs ‘factor’ column), regions (needs ‘factor’ column), another name of column (for example, ‘cell’) in the header of experimental matrix, or None. (Default: reads)
-c String regions Color the data by reads (needs ‘factor’ column), regions (needs ‘factor’ column), another name of column (for example, ‘cell’) in the header of experimental matrix, or None. (Default: regions)
-s String  None Sort the data by reads (needs ‘factor’ column), regions (needs ‘factor’ column), another name of column (for example, ‘cell’) in the header of experimental matrix, or None. (Default:None)
-e Integer 2000 Define the extend length of interested region for plotting.(Default:2000)
-rs Integer 200 Define the readsize for calculating coverage.(Default:200)
-ss Integer 50 Define the stepsize for calculating coverage.(Default:50)
-bs Integer 100 Define the binsize for calculating coverage.(Default:100)
-sy Boolean False Share y axis for convenience of comparison.
-sx Boolean False Share x axis for convenience of comparison.
-organism String hg19 Define the organism. (Default: hg19)
-color Boolean False Define the specific colors with the given column “color” in experimental matrix. The color should be in the format of matplotlib.colors. For example, “r” for red, “b” for blue, or “(100, 35, 138)” for RGB.
-mp Boolean False Share y axis for convenience of comparison.
-nqn Boolean False Perform multiprocessing for faster computation.
-df Boolean False Show the difference of the two signals which share the same labels.The result is the subtraction of the first to the second.
-show Boolean False Show the figure in the screen.
-table Boolean False Store the tables of the figure in text format.
Outputs:

In the folder with the given name (-t), you can find the following files:

  • index.html: The webpage displays all the graphics and statistical result.
  • parameters.txt: Record the time, user, commands with given arguments and processing time.
  • Some graphics in png and pdf format.