Data Visualization¶
- Allele frequency or MSA plot
- Plot text on bar plot
- Generate base editor score tracks
- Upload colorful bed files to protein paint
- Convert bed files to vcf
- Plot Venn diagram given two bed files
- Boxplot
- Plot bw file correlation
- Data table operations
- Gene expression heatmap
- Heatmap Basic
- HiC data visualization
- Plot motif position density on peaks
- Plot Chromsome Ideogram
- Interactive heatmap
- Simple lineplot
- line_plot to compare editing outcome frequency (two groups)
- Overlapping Barplot
- Pathway visualization
- Visualizing high-dimentional data using PCA or UMAP
- Correlation heatmap
- Re-order Correlation heatmap
- Plot Enrichment dotplot
- Creat data table of tracks on protein paint
- Creating facet table for protein paint
- Plot replicate correlation
- Plot correlation scatter plots
- Scatter plot by color, shape, and size
- Average signal and heatmap over a bed file
- Average signal over multiple peaks
- Average signal for multiple bw over one bed
- Statistical test on 2 signals
- Table to heatmap, no clustering
- Volcano plot for logFC and P-value/FDR
Typical Usage¶
Step 0: Load python version 2.7.13.
$ module load python/2.7.13
Step 1: Plot your figure.
$ HemTools [subcmd] -f input_data
You can always see all available sub-commands by:
$ HemTools -h
Report bug¶
Most visualizations are done interactively. Error message will be displayed directly on your screen. Please copy those error msgs and email me, Yichao.Li@stjude.org.
Note
HemTools report_bug will not work in most data visualization subcmds.