- document»
- Abstract
- Edit on GitHub
This tool creates a profile for fractional sets of genomic regions. Usually these regions are genes, but any other region defined in BED can be used. Requires a matrix generated by computeMatrix.
use: Abstract [--matrix file matrix file] --Output file name the name of the external file [--outFileSortedRegions document] [--file name output external file name data] [--resolution part of the news] [--average average] [--group Huaxia University of Science and Technology] [--outline] [--Please help] [--Version] [--average guy {the meaning is,the median,minute,maximum,standard,and}] [--plot height Plot level] [--Plot width Floor width] [--type of drawing {line,puna,and,standard,overlapping lines,heat map}] [--color color [color ...]] [--number of plots per line NUMPLOTSPERROW] [--An example of using a cluster Using pattern clustering [Using pattern clustering ...]] [--initial marker initial marker] [--end mark end mark] [--reference point mark reference mark] [--label rotation label rotation] [--area designation area designation [area designation ...]] [--sample label sample label [sample label ...]] [--plot address land] [--Y axis label minor axis label] [--and minutes YMIN [YMIN ...]] [--maximum YMAX [YMAX ...]] [--the position of legend {the best,excellent-normal,excellent-Lewy,excellent-Center,reduction-Lewy,reduction-normal,reduction-Center,Center,Center-Lewy,Center-normal,Yes}] [--each group] [--drawing file format] [--long lasting]
required parameters¶
| --matrix_file, -m | |
| Matrix files from computeMatrix. | |
| --out-filename, -out, -o | |
| The name of the file where you want to save the image. The end of the file will be used to determine the image format. Options are "png", "eps", "pdf" and "svg", e.g. MyHeatmap.png. | |
exit options¶
| --outFileSortedRegions | |
| The name of the file where the region will be saved after crossing the zero or min/max threshold. The order of the regions in the file follows the selected sort order. This is useful, for example, to generate other heatmaps while preserving the order of the first heatmap. Example: Heatmap1sortedRegions.bed | |
| --outFileNameData | |
| The name of the core data file used to save the average profile, eg MyProfile.tab. | |
| --dpi | Set DPI to save graphics. |
Parameters of clustering¶
| --k means | Number of clusters to count. When this option is set, the k-means algorithm is used to partition the matrix into clusters. It only applies to unclustered data, otherwise only the first group will be clustered. If a more accurate clustering method is required, save the base array and run the clustering using other software. If the cluster has very few members compared to the total number or area, cluster plotting may fail with an error. |
| --hklust | Number of clusters to count. When this option is set, the array will be clustered using "split join" using a hierarchical clustering algorithm. It only applies to unclustered data, otherwise only the first group will be clustered. --hclust can be very slow if you have >1000 regions. In these cases, you may prefer --kmeans, or if you need more clustering methods, you can save the underlying array and run the clustering with other software. If the cluster has very few members compared to the total number of regions, cluster plotting may fail with an error. |
| - outline | Calculate the contour score of the region. This only applies when clustering is done. The silhouette score measures how similar a region is to other regions in the same cluster as opposed to regions in other clusters. This will be reported in the last column of the region's BED file. Contour estimation can be very slow when regions exceed 100,000. |
selection parameters¶
| - Version | Display the program version number and exit |
| --middle type | Possible choices: mean, median, min, max, standard deviation, sum The type of statistics that should be used for the configuration file. Options are: average, median, min, max, sum and standard. |
| --height of the plot | Plot height in centimeters. |
| --chart width | Plot width in centimeters. The minimum value is 1 cm. |
| -- chart type | Possible choices: lines, fill, se, std, overlapping lines, heatmap "Line" will draw a contour according to the selected average type. "Fill" fills the area between zero and the contour curve. The fill color is transparent to distinguish the different profiles. "se" and "std" color the area between the profile and the standard error or standard deviation of the data. As with the fill, use a semi-transparent color. "overlapped_lines" plots the values of each region, one above the other. "heatmap" draws a cumulative heat map. |
| - color | List of colors used to plot the lines (note: "--plotType overlapping lines" is not affected). Accepts color names and HTML hex strings (for example, #eeff22). Color names should be separated by a space. For example -- the colors red blue green |
| --number of plots per row | |
| number of plots in a row | |
| --clusterUsingSamples | |
| List of sample numbers (in matrix order) to be used for clustering using -kmeans or -hclust, if not specified all samples are considered a cluster. Example: –ClusterUsingSamples 1 3 | |
| --startLabel | [region scaling mode only] A label that represents the beginning of a region on the chart. The default is TSS (transcription start site), but can be changed to anything, such as "peak start". The same applies to the --endLabel option. see below. |
| --endLabel | [scale-region-mode only] Show labels at the end of regions in the chart. By default, TES (transcription termination site). |
| --refPointLabel | |
| [Reference Point Mode Only] Mark displayed on the reference point map. The default value is the same as the selected reference point (eg TSS) but can be anything eg "peak start". | |
| --label rotation | |
| X-axis label rotation in degrees. The default value is 0, a positive value means counter-clockwise rotation. | |
| --label region, -z | |
| Region labels applied to the heat map. When drawing multiple regions, a space-separated list of labels is required. Quotation marks are required if the tag itself contains spaces. For example --regionsLabel label_1,"label 2". | |
| --Sample mark | Draw marks for the patterns. By default, the sample file name is used. If the labels themselves contain spaces, the sample labels should be separated by spaces and quoted --samplesLabel label-1 "Label 2" |
| --store address, -T | |
| The title of the chart that will be printed on the resulting image. Leave blank if there is no title. | |
| --y axis label, -y | |
| Y-axis label for the top panel. | |
| --yMin | Minimum value for the Y axis. Multiple values can be set for each profile separated by spaces. If the number of yMin values is less than the number of graphs, those values will be recycled. |
| --yMaks | Maximum value for the Y-axis. Multiple values can be set for each profile separated by spaces. If the number of yMin values is less than the number of graphs, those values will be recycled. |
| --legendLocation | |
Possible choices: top, top right, top left, top center, bottom left, bottom right, bottom center, center, center left, center right, nothing The position of the legend in the summary diagram. Note that the "none" option is not available for analyzers. | |
| -- per group | By default, all region groups are drawn according to the pattern. Use this option instead of plotting all samples per region group. Note that this is only useful if you have multiple zone groups. By sample, not by group. |
| --plotFormatPliku | |
Possible choices: png, pdf, svg, eps, plotly Image format type. If given, this option will override the image format based on the end of the plotFile. Available options are: "png", "eps", "pdf", "plotly" and "svg" | |
| --long | If set, warning messages and additional information are displayed. |
Example usage is: plotProfile -m
Detail¶
asgraph heat graph,AbstractJust take the compression matrix it producesCalculation matrixand turn it into a summary chart.
In addition to a large number of parameters for visualization optimization, you can also export the basic values of the configuration file as a table.
| Additional output type | Order | Calculation matrix | graph heat graph | Abstract |
| The base value of the heat map | --outFileNameMatrix | So | So | NO |
| Profile values | --outFileNameData | NO | So | So |
| Sort and/or filter fields | --outFileSortedRegions | So | So | So |
Advice
For more information on optional output, see the exampleCalculation matrix.
Example of use¶
The following example shows the signal profile of hg19 transcripts for our ENCODE assay data set. Note that the matrix contains sets of regions (in this case, one region for each chromosome).
# Run the compute matrix to collect the data needed for plotting $ computeMatrix scale-regions -S H3K27Me3-input.bigWig \ H3K4Me1-Input.bigWig \ H3K4Me3-Input.bigWig \ -R genes19.bed genesX.bed \ --beforeRegionStartLength 3000 \ - -regionBodyLength 5000 \ --afterRegionStartLength 3000 --skipZeros -o matrix.mat.gz$ plotProfile -m matrix.mat.gz \ -out ExampleProfile1.png \ --numPlotsPerRow 2 \ --plotTitle "Test data profile"
AbstractThere are many options, including changing the type of line drawn and the ability to draw in groups instead of patterns.
Here is the same data set, but plotted with a different set of parameters.
$ plotProfile -m matrix.mat.gz \ -out ExampleProfile2.png \ --plotType=fill \ # add color between x axis and lines --perGroup \ # create one image per BED file instead of bigWig file --color red yellow blue \ --plotTitle "Test data profile"
In another example, the data are grouped into two groups using k-means.
$ plotProfile -m matrix.mat.gz \ --perGroup \ --kmeans 2 \ -out ExampleProfile3.png
Here is the same data, but visualized with–plotType heatmap
$ plotProfile -m matrix.mat.gz \ --perGroup \ --kmeans 2 \ -plotType heatmap \ -out ExampleProfile3.png
| galaxy deepTools. | code@github. |