hclust2.py做聚类热图-基于MetaPhlAn结果或类似结构数据

 MetaPhlAn怎么安装使用看这里： 202310-宏基组学物种分析工具-MetaPhlAn4安装和使用方法-Anaconda3- centos9 stream-CSDN博客

数据格式

MetaPhlAn运行完成后合并物种丰度结果，相同结构的矩阵也可以画聚类热图

head merged_abundance_class.txt

#直接出来的结果没有对齐使用excel给大家看直观一点

分析作图

###就这么简单
source activate metaphlan4
hclust2.py -i merged_metaphlan_tables_class.txt -o merged_class.png

怎么样？ 很简单吧，其实作图就是这么简单，但实际上这个脚本还有很多其他参数，这些参数可以帮助大家对图片色彩，标签字体大小，聚类情况等做详细调整。大家在作图过程中需要根据自己情况进行反复调整。

 

出图结果

下面就是出图结果，其他的自己看吧，

 

全参数帮助信息 

###hclust2.py完整帮助文件：

hclust2.py -h

usage: hclust2.py [-h] [-i [INPUT_FILE]] [-o [OUTPUT_FILE]]
                  [--legend_file [LEGEND_FILE]] [-t INPUT_TYPE] [--sep SEP]
                  [--out_table OUT_TABLE] [--fname_row FNAME_ROW]
                  [--sname_row SNAME_ROW] [--metadata_rows METADATA_ROWS]
                  [--skip_rows SKIP_ROWS] [--sperc SPERC] [--fperc FPERC]
                  [--stop STOP] [--ftop FTOP] [--def_na DEF_NA]
                  [--f_dist_f F_DIST_F] [--s_dist_f S_DIST_F]
                  [--load_dist_matrix_f LOAD_DIST_MATRIX_F]
                  [--load_dist_matrix_s LOAD_DIST_MATRIX_S]
                  [--load_pickled_dist_matrix_f LOAD_PICKLED_DIST_MATRIX_F]
                  [--load_pickled_dist_matrix_s LOAD_PICKLED_DIST_MATRIX_S]
                  [--save_pickled_dist_matrix_f SAVE_PICKLED_DIST_MATRIX_F]
                  [--save_pickled_dist_matrix_s SAVE_PICKLED_DIST_MATRIX_S]
                  [--no_fclustering] [--no_plot_fclustering]
                  [--no_sclustering] [--no_plot_sclustering]
                  [--flinkage FLINKAGE] [--slinkage SLINKAGE] [--dpi DPI] [-l]
                  [--title TITLE] [--title_fontsize TITLE_FONTSIZE] [-s]
                  [--no_slabels] [--minv MINV] [--maxv MAXV] [--no_flabels]
                  [--max_slabel_len MAX_SLABEL_LEN]
                  [--max_flabel_len MAX_FLABEL_LEN]
                  [--flabel_size FLABEL_SIZE] [--slabel_size SLABEL_SIZE]
                  [--fdend_width FDEND_WIDTH] [--sdend_height SDEND_HEIGHT]
                  [--metadata_height METADATA_HEIGHT]
                  [--metadata_separation METADATA_SEPARATION]
                  [--colorbar_font_size COLORBAR_FONT_SIZE]
                  [--image_size IMAGE_SIZE]
                  [--cell_aspect_ratio CELL_ASPECT_RATIO]
                  [-c {Blues,BrBG,BuGn,BuPu,GnBu,Greens,Greys,OrRd,Oranges,PRGn,PiYG,PuBu,PuBuGn,PuOr,PuRd,Purples,RdBu,RdGy,RdPu,RdYlBu,RdYlGn,Reds,Spectral,YlGn,YlGnBu,YlOrBr,YlOrRd,afmhot,autumn,binary,bone,brg,bwr,cool,copper,flag,gist_earth,gist_gray,gist_heat,gist_ncar,gist_rainbow,gist_stern,gist_yarg,gnuplot,gnuplot2,gray,hot,hsv,jet,ocean,pink,prism,rainbow,seismic,spectral,spring,summer,terrain,winter,bbcyr,bbcry,bcry}]
                  [--bottom_c BOTTOM_C] [--top_c TOP_C] [--nan_c NAN_C]

TBA

optional arguments:
  -h, --help            show this help message and exit
  -i [INPUT_FILE], --inp [INPUT_FILE], --in [INPUT_FILE]
                        The input matrix
  -o [OUTPUT_FILE], --out [OUTPUT_FILE]
                        The output image file [image on screen of not
                        specified]
  --legend_file [LEGEND_FILE]
                        The output file for the legend of the provided
                        metadata
  -t INPUT_TYPE, --input_type INPUT_TYPE
                        The input type can be a data matrix or distance matrix
                        [default data_matrix]

Input data matrix parameters:
  --sep SEP
  --out_table OUT_TABLE
                        Write processed data matrix to file
  --fname_row FNAME_ROW
                        row number containing the names of the features
                        [default 0, specify -1 if no names are present in the
                        matrix
  --sname_row SNAME_ROW
                        column number containing the names of the samples
                        [default 0, specify -1 if no names are present in the
                        matrix
  --metadata_rows METADATA_ROWS
                        Row numbers to use as metadata[default None, meaning
                        no metadata
  --skip_rows SKIP_ROWS
                        Row numbers to skip (0-indexed, comma separated) from
                        the input file[default None, meaning no rows skipped
  --sperc SPERC         Percentile of sample value distribution for sample
                        selection
  --fperc FPERC         Percentile of feature value distribution for sample
                        selection
  --stop STOP           Number of top samples to select (ordering based on
                        percentile specified by --sperc)
  --ftop FTOP           Number of top features to select (ordering based on
                        percentile specified by --fperc)
  --def_na DEF_NA       Set the default value for missing values [default None
                        which means no replacement]

Distance parameters:
  --f_dist_f F_DIST_F   Distance function for features [default correlation]
  --s_dist_f S_DIST_F   Distance function for sample [default euclidean]
  --load_dist_matrix_f LOAD_DIST_MATRIX_F
                        Load the distance matrix to be used for features
                        [default None].
  --load_dist_matrix_s LOAD_DIST_MATRIX_S
                        Load the distance matrix to be used for samples
                        [default None].
  --load_pickled_dist_matrix_f LOAD_PICKLED_DIST_MATRIX_F
                        Load the distance matrix to be used for features as
                        previously saved as pickle file using hclust2 itself
                        [default None].
  --load_pickled_dist_matrix_s LOAD_PICKLED_DIST_MATRIX_S
                        Load the distance matrix to be used for samples as
                        previously saved as pickle file using hclust2 itself
                        [default None].
  --save_pickled_dist_matrix_f SAVE_PICKLED_DIST_MATRIX_F
                        Save the distance matrix for features to file [default
                        None].
  --save_pickled_dist_matrix_s SAVE_PICKLED_DIST_MATRIX_S
                        Save the distance matrix for samples to file [default
                        None].

Clustering parameters:
  --no_fclustering      avoid clustering features
  --no_plot_fclustering
                        avoid plotting the feature dendrogram
  --no_sclustering      avoid clustering samples
  --no_plot_sclustering
                        avoid plotting the sample dendrogram
  --flinkage FLINKAGE   Linkage method for feature clustering [default
                        average]
  --slinkage SLINKAGE   Linkage method for sample clustering [default average]

Heatmap options:
  --dpi DPI             Image resolution in dpi [default 150]
  -l, --log_scale       Log scale
  --title TITLE         Title of the plot
  --title_fontsize TITLE_FONTSIZE
                        Font size of the title
  -s, --sqrt_scale      Square root scale
  --no_slabels          Do not show sample labels
  --minv MINV           Minimum value to display in the color map [default
                        None meaning automatic]
  --maxv MAXV           Maximum value to display in the color map [default
                        None meaning automatic]
  --no_flabels          Do not show feature labels
  --max_slabel_len MAX_SLABEL_LEN
                        Max number of chars to report for sample labels
                        [default 15]
  --max_flabel_len MAX_FLABEL_LEN
                        Max number of chars to report for feature labels
                        [default 15]
  --flabel_size FLABEL_SIZE
                        Feature label font size [default 10]
  --slabel_size SLABEL_SIZE
                        Sample label font size [default 10]
  --fdend_width FDEND_WIDTH
                        Width of the feature dendrogram [default 1 meaning
                        100% of default heatmap width]
  --sdend_height SDEND_HEIGHT
                        Height of the sample dendrogram [default 1 meaning
                        100% of default heatmap height]
  --metadata_height METADATA_HEIGHT
                        Height of the metadata panel [default 0.05 meaning 5%
                        of default heatmap height]
  --metadata_separation METADATA_SEPARATION
                        Distance between the metadata and data panels.
                        [default 0.001 meaning 0.1% of default heatmap height]
  --colorbar_font_size COLORBAR_FONT_SIZE
                        Color bar label font size [default 12]
  --image_size IMAGE_SIZE
                        Size of the largest between width and eight size for
                        the image in inches [default 8]
  --cell_aspect_ratio CELL_ASPECT_RATIO
                        Aspect ratio between width and height for the cells of
                        the heatmap [default 1.0]
  -c {Blues,BrBG,BuGn,BuPu,GnBu,Greens,Greys,OrRd,Oranges,PRGn,PiYG,PuBu,PuBuGn,PuOr,PuRd,Purples,RdBu,RdGy,RdPu,RdYlBu,RdYlGn,Reds,Spectral,YlGn,YlGnBu,YlOrBr,YlOrRd,afmhot,autumn,binary,bone,brg,bwr,cool,copper,flag,gist_earth,gist_gray,gist_heat,gist_ncar,gist_rainbow,gist_stern,gist_yarg,gnuplot,gnuplot2,gray,hot,hsv,jet,ocean,pink,prism,rainbow,seismic,spectral,spring,summer,terrain,winter,bbcyr,bbcry,bcry}, --colormap {Blues,BrBG,BuGn,BuPu,GnBu,Greens,Greys,OrRd,Oranges,PRGn,PiYG,PuBu,PuBuGn,PuOr,PuRd,Purples,RdBu,RdGy,RdPu,RdYlBu,RdYlGn,Reds,Spectral,YlGn,YlGnBu,YlOrBr,YlOrRd,afmhot,autumn,binary,bone,brg,bwr,cool,copper,flag,gist_earth,gist_gray,gist_heat,gist_ncar,gist_rainbow,gist_stern,gist_yarg,gnuplot,gnuplot2,gray,hot,hsv,jet,ocean,pink,prism,rainbow,seismic,spectral,spring,summer,terrain,winter,bbcyr,bbcry,bcry}
  --bottom_c BOTTOM_C   Color to use for cells below the minimum value of the
                        scale [default None meaning bottom color of the scale]
  --top_c TOP_C         Color to use for cells below the maximum value of the
                        scale [default None meaning bottom color of the scale]
  --nan_c NAN_C         Color to use for nan cells [default None]

常用调整参数

  --stop 当样品数太多，也就是列数太多，可选择自己希望显示丰度最高的前多个个样品
  --ftop 当物种数太多，也就是行数太多，可以选择自己希望显示的丰度最高的多少个物种

--dpi  这个很重要哦，当行列数比较多时需要自己调整整个输出图的画幅以适应实际需求

--flabel_size        这里就是行头物种名标签在图片中的大小，

--slabel_size        同样这里是表头中样品名标签在图片中的大小。

--cell_aspect_ratio        这个就是上面显示的每个方格的长和宽的比例，默认为1:1也就是方块，0.5也即是横向的长方形了，2就成了纵向的长方形了，这个可以将图调整成合适的比例显示。

--no_fclustering        --no_sclustering         这个很重要，有时候不想查看样品之间的聚类情况，使用--no_clustering后图中的样品会按顺序出现在图中，同样--no_fclustering则是不进行物种的聚类。

-c 这个参数是指图片显示色彩的体系，默认为红-蓝色系，可以指定其他的，自己试着选就行了。

其他的大家参考全参数帮助文件吧，大家对照着调整即可；个人一般会反复调整到合适的比例和色彩