hclust2 1.0.0

Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publication

Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publication.

Installation

$ conda install -c bioconda hclust2

Examples

Below is the heatmap produced by Hclust2 on the MetaPhlAn2 abundance profiles of HMP and HMP1-phase2 samples (microbial species and samples are hierarchically clustered).

Usage

#!python

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_sclustering] [--flinkage FLINKAGE]
                  [--slinkage SLINKAGE] [--dpi DPI] [-l] [--title TITLE] [-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]
                  [--image_size IMAGE_SIZE]
                  [--cell_aspect_ratio CELL_ASPECT_RATIO]
                  [-c {Accent,Blues,BrBG,BuGn,BuPu,Dark2,GnBu,Greens,Greys,OrRd,Oranges,PRGn,Paired,Pastel1,Pastel2,PiYG,PuBu,PuBuGn,PuOr,PuRd,Purples,RdBu,RdGy,RdPu,RdYlBu,RdYlGn,Reds,Set1,Set2,Set3,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]

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_sclustering      avoid clustering samples
  --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
  -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]
  --image_size IMAGE_SIZE
                        Size of the largest between width and eight size for

  --cell_aspect_ratio CELL_ASPECT_RATIO
                        Aspect ratio between width and height for the cells of
                        the heatmap [default 1.0]
  -c {Accent,Blues,BrBG,BuGn,BuPu,Dark2,GnBu,Greens,Greys,OrRd,Oranges,PRGn,Paired,Pastel1,Pastel2,PiYG,PuBu,PuBuGn,PuOr,PuRd,Purples,RdBu,RdGy,RdPu,RdYlBu,RdYlGn,Reds,Set1,Set2,Set3,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 {Accent,Blues,BrBG,BuGn,BuPu,Dark2,GnBu,Greens,Greys,OrRd,Oranges,PRGn,Paired,Pastel1,Pastel2,PiYG,PuBu,PuBuGn,PuOr,PuRd,Purples,RdBu,RdGy,RdPu,RdYlBu,RdYlGn,Reds,Set1,Set2,Set3,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]