plot-multi
Plots taxonomic composition across multiple Kraken reports. Supports stacked bar charts and bubble charts.
Syntax
kraut plot-multi [OPTIONS] INPUT_FILES...
Arguments
| Argument |
Type |
Description |
INPUT_FILES... |
PATH |
Required. One or more Kraken report files. |
Options
| Option |
Short |
Type |
Description |
--output |
-o |
PATH |
Required. Output plot file. |
--rank |
-r |
TEXT |
Taxonomic rank to plot (default: S). |
--metric |
-m |
TEXT |
Metric: TOT or LVL (default: TOT). |
--kind |
|
TEXT |
Plot kind: stacked or bubble (default: stacked). |
--min-perc |
|
FLOAT |
Fold taxa below this % abundance into “Others” (default: 1.0). |
--top-taxa |
|
INTEGER |
Keep top N taxa and fold others into “Others” (default: 0). |
--no-unclassified |
|
|
Exclude unclassified reads. |
--title |
|
TEXT |
Plot title. |
Examples
Stacked bar chart of multiple samples
kraut plot-multi reports/*.krep -o stacked_bars.png
Interactive bubble chart
kraut plot-multi reports/*.krep --kind bubble -o bubbles.html
Focusing on top 10 Genera
kraut plot-multi reports/*.krep -r G --top-taxa 10 -o top_genera.png
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