--plotType {lines,fill,se,std}                        "lines" will plot the profile line based on the                        average type selected. "fill" fills the region between                        zero and the profile curve. The fill in color is semi                        transparent to distinguish different profiles. "se"                        and "std" color the region between the profile and the                        standard error or standard deviation of the data.                        (default: lines)  --sortUsingSamples SORTUSINGSAMPLES [SORTUSINGSAMPLES ...]                        List of sample numbers (order as in matrix), which are                        used by --sortUsing for sorting. If no value is set,                        it uses all samples. Example: --sortUsingSamples 1 3                        (default: None)  --linesAtTickMarks    Draw dashed lines from all tick marks through the                        heatmap. This is then similar to the dashed line draw                        at region bounds when using a reference point and                        --sortUsing region_length (default: False)  --clusterUsingSamples CLUSTERUSINGSAMPLES [CLUSTERUSINGSAMPLES ...]                        List of sample numbers (order as in matrix), that are                        used for clustering by --kmeans or --hclust if not
                        given, all samples are taken into account for                        clustering. Example: --ClusterUsingSamples 1 3                        (default: None)  --averageTypeSummaryPlot {mean,median,min,max,std,sum}                        Define the type of statistic that should be plotted in                        the summary image above the heatmap. The options are:                        "mean", "median", "min", "max", "sum" and "std".                        (default: mean)  --missingDataColor MISSINGDATACOLOR                        If --missingDataAsZero was not set, such cases will be                        colored in black by default. Using this parameter, a                        different color can be set. A value between 0 and 1                        will be used for a gray scale (black is 0). For a list                        of possible color names see: http://packages.python.or                        g/ete2/reference/reference_svgcolors.html. Other                        colors can be specified using the #rrggbb notation.                        (default: black)  --colorNumber COLORNUMBER                        N.B., --colorList is required for an effect. This                        controls the number of transitions from one color to                        the other. If --colorNumber is the number of colors in                        --colorList then there will be no transitions between                        the colors. (default: 256)  --heatmapHeight HEATMAPHEIGHT                        Plot height in cm. The default for the heatmap height                        is 28. The minimum value is 3 and the maximum is 100.                        (default: 28)  --heatmapWidth HEATMAPWIDTH                        Plot width in cm. The default value is 4 The minimum                        value is 1 and the maximum is 100. (default: 4)

computeMatrix  reference-point  --referencePoint  TSS  -p 15 -b 10000 -a 10000 -R gene.bed -S  test.bw  --skipZeros --missingDataAsZero   -o test_TSS.gz  --outFileSortedRegions test_genes.bed

reference-point # 选择模式 -p 15 # 线程数 --referencePoint TSS  # 选择参考点，还可以选择TES, center -b 10000 -a 10000  # 感兴趣的区域，-b上游，-a下游 -R  # 基因注释信息 -S  # 提供的 bigwig 文件 --skipZeros  # 是否包含零分区域--missingDataAsZero # 不显示0的数据

If set, missing data (NAs) will be treated as zeros.                        The default is to ignore such cases, which will be                        depicted as black areas in a heatmap. (see the                        --missingDataColor argument of the plotHeatmap command                        for additional options). (default: False)