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Sample output:
Plot distribution
Usage
usage: ./plot_distribution.R [-h] [-bw BINWIDTH] [--xlab XLAB] [--ylab YLAB]
[--width WIDTH] [--height HEIGHT] [-t title]
infile outfile
Plot distribution.Infile should be a tsv file of two columns (group and "value")
positional arguments:
infile infile
outfile outfile
optional arguments:
-h, --help show this help message and exit
-bw BINWIDTH, --binwidth BINWIDTH
binwidth
--xlab XLAB xlabel
--ylab YLAB ylabel
--width WIDTH output image width [20]
--height HEIGHT output image height [5]
-t title, --title title
title
Sample output:
Distribution plot using seaborn
Example: distribution of sequence length
cat ../sequence/seq.fa | fasta2tab -l | cut -f 3 | \
plot_distribution.py -t "Disribution of sequence length" -x "sequence length" -o pic.png
Sample output:
Plot heatmap with pheatmap
Usage
usage: ./plot_heatmap.R [-h] [-H] [-F field_seperator] [-a] [-al]
[--title title] [-s scale] [-ncr] [-ncc] [-c color]
[-nrc] [--width width] [--height height]
[-thr treeheight_row] [-thc treeheight_col]
[-fo fontsize] [-fr fontsize_row] [-fc fontsize_col]
infile outname
Plot heatmap. Infile should be a csv/tsv file with header containing column names. Annotation for row is also supported, please put them in the last column.
positional arguments:
infile infile (tsv, with head
outname outname
optional arguments:
-h, --help show this help message and exit
-H, --header header
-F field_seperator, --field-seperator field_seperator
field seperator
-a, --with-annot add annotation_row from the last column
-al, --with-annot-legend
show annotation_row_legend
--title title title
-s scale, --scale scale
scale. row | column | none [row]
-ncr, --not-cluster-rows
do not cluster_rows
-ncc, --not-cluster-cols
do not cluster_cols
-c color, --color color
sequential palettes names [RdYlBu]
-nrc, --not-reverse-color-order
do not reverse color order
--width width output image width
--height height output image height
-thr treeheight_row, --treeheight_row treeheight_row
treeheight_row
-thc treeheight_col, --treeheight_col treeheight_col
treeheight_col
-fo fontsize, --fontsize fontsize
fontsize
-fr fontsize_row, --fontsize_row fontsize_row
fontsize_row
-fc fontsize_col, --fontsize_col fontsize_col
fontsize_col
Sample output:
