categorized_dist_scatterplot.py – makes a figure representing average distances between samples, broken down by categories. I call it a ‘categorized distance scatterplot’¶
Description:
makes a figure representing average distances between samples, broken down by categories. I call it a ‘categorized distance scatterplot’. See script usage for more details. The mapping file specifies the relavent data - if you have e.g. ‘N/A’ values or samples you don’t want included, first use filter_samples_from_otu_table.py to remove unwanted samples from the mapping file, and thus the analysis. Note that the resulting plot will include only samples in both the mapping file AND the distance matrix.
Usage: categorized_dist_scatterplot.py [options]
Input Arguments:
Note
[REQUIRED]
- -m, --map
- Mapping file
- -d, --distance_matrix
- Distance matrix
- -p, --primary_state
- Samples matching this state will be plotted. E.g.: AgeCategory:Child . See qiime’s filter_samples_from_otu_table.py for more syntax options
- -a, --axis_category
- This will form the horizontal axis of the figure, e.g.: AgeYears . Must be numbers
- -o, --output_path
- Output figure, filename extention determines format. E.g.: “fig1.png” or similar. A “fig1.txt” or similar will also be created with the data underlying the figure
[OPTIONAL]
- -c, --colorby
- Samples will first be separated by this column of the mapping file. They will be colored by this column of the mapping file, and all comparisons will be done only among samples with the same value in this column. e.g.: Country. You may omit -c, and the samples will not be separated
- -s, --secondary_state
- All samples matching the primary state will be compared to samples matcthing this secondary state. E.g.: AgeCategory:Adult
Output:
a figure and the text dat for that figure
Canonical Example:
Split samples by country. Within each country compare each child to all adults. Plot the average distance from that child to all adults, vs. the age of that child
python categorized_dist_scatterplot.py -m map.txt -d unifrac_distance.txt -c Country -p AgeCategory:Child -s AgeCategory:Adult -a AgeYears -o fig1.png
Example 2:
Same as above, but compares Child with all other categories (e.g.: NA, Infant, etc.)
python categorized_dist_scatterplot.py -m map.txt -d unifrac_distance.txt -c Country -p AgeCategory:Child -a AgeYears -o fig1.svg