Metadata-Version: 2.1
Name: hclust2
Version: 1.0.0
Summary: Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publication
Home-page: http://github.com/SegataLab/hclust2/
Author: Francesco Asnicar
Author-email: f.asnicar@unitn.it
License: UNKNOWN
Description: 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).
        
        ![Optimized-hmp_profiling_background.png](https://bitbucket.org/repo/gy6GaR/images/1429983578-Optimized-hmp_profiling_background.png)
        
        # 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]
        
        ```
        
Platform: UNKNOWN
Description-Content-Type: text/markdown
