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- graph heat graph
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- required parameters
- exit options
- Parameters of clustering
- selection parameters
- Detail
- Example of use
- More colors for the heat map
- The heat map is not framed
This tool creates heat maps of results associated with genomic regions. The program requires a matrix file generated by the toolCalculation matrix.
use: graph heat graph [--matrix file matrix file] --Output file name the name of the external file [--outFileSortedRegions document] [--field of output filenames document] [--Interpolation elasticity] [--resolution part of the news] [--average average] [--group Huaxia University of Science and Technology] [--outline] [--Please help] [--Version] [--type of drawing {line,puna,and,standard}] [--Sort area {reduction,to get up,NO,Keep}] [--Sort by {the meaning is,the median,maximum,minute,and,the length of the area}] [--Sort by patterns Classification patterns [Classification patterns ...]] [--Check mark] [--An example of using a cluster Using pattern clustering [Using pattern clustering ...]] [--mediumTypeSummaryPlot {the meaning is,the median,minute,maximum,standard,and}] [--without color data without color data] [--color card color card [color card ...]] [--A A] [--list of colors color card [color card ...]] [--Color Color] [--minimum value minimum value [minimum value ...]] [--z max ZMAX [ZMAX ...]] [--the height of the heat map the height of the heat map] [--the width of the heat map the width of the heat map] [--See the contents {conspiracy, heat map and colored strips,conspiracy and heat map,heat map Only,heat map and colored strips}] [--boxAround popularity map BOXAROUND heat map] [--axis x label Mark X axis] [--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 | |
| --outFileNameMatrix | |
| If this option is given, the matrix of values under the heatmap will be saved with this name, eg mymatrix.gz. | |
| --interpolation method | |
Possible choices: Automatic, Closest, Bilinear, Bicubic, Gaussian If the heatmap image contains a large number of columns, it is usually better to use the interpolation method for better results (seehttps://matplotlib.org/examples/images_contours_and_fields/interpolation_methods.html) By default plotHeatmap uses the methodlastIf the number of columns is 1000 or less. Otherwise, it uses the bilinear method. This default behavior can be changed with any of the following options: "closest", "bilinear", "bicubic", "gaussian" | |
| --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 |
| -- chart type | Possible choices: crte, fill, se, std "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. |
| --sortRegion | Possible choices: down, up, no, wait Specifies whether the heatmap should display sorted areas. By default, sorting is in descending order based on the average value of each region. Note that "keep" and "don't" are the same thing. |
| -- sort by | Possible choices: average, median, maximum, minimum, sum, region length Specify which method should be used for sorting. The method is evaluated for each row. For region_length, draw a dashed line at the end of the region (TSS reference points and center) or at the beginning of the region (TES reference point). |
| --sortUsingSamples | |
| List of number patterns (in matrix order) used by --sortUsing to sort. If no value is set, all samples will be used. Example: --sortUsingSamples 1 3 | |
| --linesAtTickMarks | |
| Draw dashed lines from all the markers using the heat map. This is similar to dashed lines drawn on region boundaries using a reference point and the --sortUsing region_length option | |
| --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 | |
| --AverageTypeSummaryPlot | |
Possible choices: mean, median, min, max, standard deviation, sum Specifies the type of statistics that should be displayed in the summary image above the heatmap. Options are: average, median, min, max, sum and standard. | |
| -- no data color | |
| If the --missingDataAsZero option is not set, this case is displayed in black by default. Different colors can be set using this parameter. For shades of gray, a value between 0 and 1 will be used (black is 0). For a list of possible color names, see:http://packages.python.org/ete2/reference/reference_svgcolors.html.Other colors can be specified using the #rrggbb tag. | |
| -- color map | The color map that will be used in the heat map. If multiple heatmaps are printed, the color of each heatmap can be entered separately (e.g.--colorMap red-blue).If the number of colormaps is less than the number of drawn heatmaps, the colormaps will be recycled. You can see the available values here:http://matplotlib.org/users/colormaps.htmlAvailable options are: 'magma', 'inferno', 'plasma', 'viridis', 'cividis', 'twilight', 'twilight_shifted', 'turbo', 'Blues', 'BrBG', 'BuGn', 'BuPu ', 'CMRmap', 'GnBu', 'Green', 'Grey', 'OrRd', 'Orange', 'PRGn', 'PiYG', 'PuBu', 'PuBuGn', 'PuOr', 'PuRd', "Purple", "RdBu", "RdGy", "RdPu", "RdYlBu", "RdYlGn", "Red", "Spectre", "Wistia", "YlGn", "YlGnBu", "YlOrBr", "YlOrRd ', 'afmhot', 'autumn', 'binary', 'bone', 'brg', 'bwr', 'cool', 'coolwarm', 'copper', 'cubehelix', 'flag', 'gist_earth', "gist_gray", "gist_heat", "gist_ncar", "gist_rainbow", "gist_stern", "gist_yarg", "gnuplot", "gnuplot2", "gray", "hot", "hsv", "jet", " nipy_spectral ', 'ocean', 'pink', 'prism', 'rainbow', 'seismic', 'spring', 'summer', 'terrain', 'winter', 'Accent', 'Dark2', 'Matched', 'Pastel1', 'Pastel2', 'Set1', 'Set2', 'Set3', 'tab10', 'tab20', 'tab20b', 'tab20c', 'rocket', 'mako', 'vlag', ' addict ' |
| - A | The alpha channel (transparency) used in the heatmap. Default value is 1.0, value must be between 0 and 1. |
| --list of colors | List of colors used to create the color map. For example, if–colorList black, yellow, blueSet (comma-separated colors), then create a colormap that starts with black, moves to yellow, and ends with blue. If this option is checked, it will override the selected –colorMap option. You can see the list of valid color names here:http://matplotlib.org/examples/color/named_colors.htmlHexadecimal colors are valid (eg #34a2b1). If you want to specify separate colors for different heatmaps, you should separate them with spaces, for example:–colorList "white,#cccccc" "white,dark red"As for --colorMap, if the number of color lists is less than the number of drawn heatmaps, the color lists will be recycled. The number of passes is specified by the –colorNumber option. |
| --colorNumber | Note that the -colorList option is required for effect. This controls the number of transitions from one color to another. If --colorNumber is the number of colors in --colorList, there will be no transition between colors. |
| --zMin, -min | The minimum intensity value of the heat map. Multiple values can be set for each heatmap, separated by spaces. If the number of zMin values is less than the number of heatmaps, those values will be recycled. If the value is set to "auto", it will be set to the first percentile of the matrix value. |
| --zMax., -max | The maximum intensity value of the heat map. Multiple values can be set for each heatmap, separated by spaces. If the number of zMax values is less than the number of heatmaps, those values will be recycled. If the value is set to "auto", it will be set to the 98th percentile of the matrix value. |
| --heatmapHeight | |
| Plot height in centimeters. The default heatmap height is 28. The minimum value is 3 and the maximum value is 100. | |
| --heatmapWidth | Plot width in centimeters. The default is 4, the minimum is 1, and the maximum is 100. |
| --what a show | Possible choices: graph, heatmap and color bar, graph and heatmap, heatmap only, heatmap and color bar The default setting is to include a summary or profile plot on top of the heatmap and the heatmap color bar. Other options are "graph and heatmap", "heatmap only", "heatmap and colorbar" and the default "graph, heatmap and colorbar". |
| --boxAroundHeatmaps | |
| By default, a black box is drawn around the heatmap. This can be disabled by setting --boxAroundHeatmaps no | |
| --x axis label, -x | |
| Opis mark X osi | |
| --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: plotHeatmap -m
Detail¶
notes
With the release of deepTools 2.3 it is now possible to set the color and scale of each heatmap separately. We also added an option to remove the border around the heatmap.
graph heat graphwill not change these valuesCalculation matrixAfter calculations, it simply converts them into heat maps and summary diagrams. It provides a number of parameters to explore different visualizations and adjust the resulting image (see commands above).
Additionally, you can download all the datasheets from the various charts, including the regions used to generate the final chart. The following table summarizes the optional output types available for the three tools.
| 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 creates a heatmap of hg19 transcripts for our ENCODE test 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$ plotHeatmap -m matrix.mat.gz \ -out ExampleHeatmap1.png \
As previously mentioned,graph heat graphThere are many options including the ability to group k-means and change the color map.
$ plotHeatmap -m matrix_two_groups.gz \ -out ExampleHeatmap2.png \ --colorMap RdBu \ --whatToShow 'heatmap i traka boja' \ --zMin -3 --zMax 3 \ --kmeans 4
Advice
more examplesyou can find on our websiteGallery.
More colors for the heat map¶
As of deepTools 2.3, it is now possible to customize the color and scale of each heatmap. There are two ways to adjust the colors, one is to specify each color map (eg.–colorMap RdBlGr winter terrain), and another is to give each color a heatmap (eg--colorList 'red, blue' 'white, green', 'white, blue, red') In the second example, the number of transitions between colors is given by s– color numberThe default is 256.
Usage is below– List of colorsInstructions for use. The scale of each heatmap is also changed using-z minimumand-z max.
$ plotHeatmap -m matrix_two_groups.gz \ -out ExampleHeatmap3.png \ --colorList 'black,yellow' 'white,blue' '#ffffff,orange,#000000' --whatToShow 'heatmap and color bar' \ --zMin - 2 -2 0 --zMax. 2 2 3 --kmean 4 --dpi 100
The heat map is not framed¶
In version 2.3 we also added an option to remove the border around the heatmap. In the following example, we combine different colormap colors, different scales, and new ones–boxAroundHeatmapsoption.
$ plotHeatmap -m matrix_two_groups.gz \ -out PrimjerHeatmap4.png \ --colorMap Oranges_r Blues_r Greens --whatToShow 'heatmap i traka boja' \ --zMin -4 -4 0 --zMax 0 0 5 --kmeans 4 - - dpi 100 --boxAroundHeatmaps 否
Advice
more examplesyou can find on our websiteGallery.
| galaxy deepTools. | code@github. |