ATAC数据做heatmap信号热图与谱图（deeptools）

简介：本次使用的是孔老师的数据，目的想用ATAC数据中combine相对于control来说down的peak来做一组信号热图与谱图。因此bed文件使用的是提取的down的peak.bed文件。

参考以下教程

https://www.jianshu.com/p/1f38674b2475

deeptools 提供了computeMatrix命令以计算特定基因组区域的ChIP-seq信号，并通过plotHeatmap和plotProfile函数分别产生ChIP-seq信号热图与谱图。

computeMatrix

computeMatrix提供以下两种用法以不同的参考系计算ChIP-seq的信号

1. computeMatrix scale-regions ：以一段区域为参考系，将所有参考的基因组区域缩放至指定的区域长度，计算该区域内的ChIP-seq信号
2. computeMatrix reference-point：以某一坐标为参考系，取上下游一定长度作为窗口计算区域内的ChIP-seq信号值

scale-regions

(base) wu_lab@bio:~/yuanye/projects/ATACseq/kongyu/2021_11_30/bigwig$ computeMatrix scale-regions -S Control_rep1.bw EC-8042_rep1.bw Vorinostat_rep1.bw Combine_rep1.bw -R /Data/wu_lab/yuanye/projects/ATACseq/kongyu/2021_11_30/diff_peak_4vs1/combine_down.bed  --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros -o /Data/wu_lab/yuanye/projects/ATACseq/kongyu/2021_11_30/heatmap/combine_atac_down.mat.gz -p 20

–scoreFileName, -S：输入的bw文件，可以是校正后的bw文件
–regionsFileName, -R：BED/GTF 格式的文件，指定需要计算的基因组区域
–outFileName, -out, -o：输出的文件
–regionBodyLength, -m：缩放后的基因组区域长度（bp），指定的基因组区域都会被缩放至该长度
–beforeRegionStartLength, -b, --upstream：基因组区域起始位点上游需要延伸的长度（bp）
–afterRegionStartLength, -a, --downstream：基因组区域终止位点下游需要延伸的长度（bp）
–skipZeros：设置后跳过只有0的位点。

画图

(base) wu_lab@bio:~/yuanye/projects/ATACseq/kongyu/2021_11_30/heatmap$ plotHeatmap -m combine_atac_down.mat.gz -out combine_atac_down_heatmap.png --whatToShow "plot, heatmap and colorbar" --startLabel start --endLabel end

computeMatrix: https://deeptools.readthedocs.io/en/develop/content/tools/computeMatrix.html#deepBlue%20arguments
plotHeatmap: https://deeptools.readthedocs.io/en/develop/content/tools/plotHeatmap.html?highlight=plotheatmap
plotProfile: https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html?highlight=plotheatmap
deeptools gallery: https://deeptools.readthedocs.io/en/latest/content/example_gallery.html#normalized-chip-seq-signals-and-peak-regions

聚类图

如果想分成几个cluster的画

 plotHeatmap -m R8_center.gz -out R8_cluster.png  --kmeans 3  --colorMap Blues

出来的类似是这样

color 可用颜色如下
supported values are ‘Accent’, ‘Accent_r’, ‘Blues’, ‘Blues_r’, ‘BrBG’, ‘BrBG_r’, ‘BuGn’, ‘BuGn_r’, ‘BuPu’, ‘BuPu_r’, ‘CMRmap’, ‘CMRmap_r’, ‘Dark2’, ‘Dark2_r’, ‘GnBu’, ‘GnBu_r’, ‘Greens’, ‘Greens_r’, ‘Greys’, ‘Greys_r’, ‘OrRd’, ‘OrRd_r’, ‘Oranges’, ‘Oranges_r’, ‘PRGn’, ‘PRGn_r’, ‘Paired’, ‘Paired_r’, ‘Pastel1’, ‘Pastel1_r’, ‘Pastel2’, ‘Pastel2_r’, ‘PiYG’, ‘PiYG_r’, ‘PuBu’, ‘PuBuGn’, ‘PuBuGn_r’, ‘PuBu_r’, ‘PuOr’, ‘PuOr_r’, ‘PuRd’, ‘PuRd_r’, ‘Purples’, ‘Purples_r’, ‘RdBu’, ‘RdBu_r’, ‘RdGy’, ‘RdGy_r’, ‘RdPu’, ‘RdPu_r’, ‘RdYlBu’, ‘RdYlBu_r’, ‘RdYlGn’, ‘RdYlGn_r’, ‘Reds’, ‘Reds_r’, ‘Set1’, ‘Set1_r’, ‘Set2’, ‘Set2_r’, ‘Set3’, ‘Set3_r’, ‘Spectral’, ‘Spectral_r’, ‘Wistia’, ‘Wistia_r’, ‘YlGn’, ‘YlGnBu’, ‘YlGnBu_r’, ‘YlGn_r’, ‘YlOrBr’, ‘YlOrBr_r’, ‘YlOrRd’, ‘YlOrRd_r’, ‘afmhot’, ‘afmhot_r’, ‘autumn’, ‘autumn_r’, ‘binary’, ‘binary_r’, ‘bone’, ‘bone_r’, ‘brg’, ‘brg_r’, ‘bwr’, ‘bwr_r’, ‘cividis’, ‘cividis_r’, ‘cool’, ‘cool_r’, ‘coolwarm’, ‘coolwarm_r’, ‘copper’, ‘copper_r’, ‘cubehelix’, ‘cubehelix_r’, ‘flag’, ‘flag_r’, ‘gist_earth’, ‘gist_earth_r’, ‘gist_gray’, ‘gist_gray_r’, ‘gist_heat’, ‘gist_heat_r’, ‘gist_ncar’, ‘gist_ncar_r’, ‘gist_rainbow’, ‘gist_rainbow_r’, ‘gist_stern’, ‘gist_stern_r’, ‘gist_yarg’, ‘gist_yarg_r’, ‘gnuplot’, ‘gnuplot2’, ‘gnuplot2_r’, ‘gnuplot_r’, ‘gray’, ‘gray_r’, ‘hot’, ‘hot_r’, ‘hsv’, ‘hsv_r’, ‘icefire’, ‘icefire_r’, ‘inferno’, ‘inferno_r’, ‘jet’, ‘jet_r’, ‘magma’, ‘magma_r’, ‘mako’, ‘mako_r’, ‘nipy_spectral’, ‘nipy_spectral_r’, ‘ocean’, ‘ocean_r’, ‘pink’, ‘pink_r’, ‘plasma’, ‘plasma_r’, ‘prism’, ‘prism_r’, ‘rainbow’, ‘rainbow_r’, ‘rocket’, ‘rocket_r’, ‘seismic’, ‘seismic_r’, ‘spring’, ‘spring_r’, ‘summer’, ‘summer_r’, ‘tab10’, ‘tab10_r’, ‘tab20’, ‘tab20_r’, ‘tab20b’, ‘tab20b_r’, ‘tab20c’, ‘tab20c_r’, ‘terrain’, ‘terrain_r’, ‘turbo’, ‘turbo_r’, ‘twilight’, ‘twilight_r’, ‘twilight_shifted’, ‘twilight_shifted_r’, ‘viridis’, ‘viridis_r’, ‘vlag’, ‘vlag_r’, ‘winter’, ‘winter_r’