rpf_Geneplot¶

rpf_Geneplot draws per-gene RPF or RNA-seq density profiles from a merged density table.

Function¶

Use this command to visualize the nucleotide-level density profile of one gene or a list of genes across samples. The command extracts the selected gene records from a merged density table, converts frame-specific density columns into a continuous nucleotide-level profile, and writes one plot per gene.

Input¶

The input file should be a merged RPF/RNA density table with annotation columns and frame-specific sample columns, for example:

name  now_nt  from_tis  from_tts  region  codon  sample1_f0  sample1_f1  sample1_f2  ...

Gene IDs supplied with -g or -l should match the values in the name column.

Parameters¶

Parameter	Required	Meaning
`-r`	yes	Input merged RPF/RNA density file in TXT/TSV format.
`-g`	no	Single gene/transcript ID to plot. Mutually exclusive with `-l`.
`-l`	no	Gene/transcript ID list file. Each line should contain one ID. Mutually exclusive with `-g`.
`--log`	no	Set y-axis to log scale. Allowed values: `2` or `10`. Default: no log scaling.

At least one of -g or -l should be provided.

Output¶

For each gene/transcript, the command writes two plot files in the current working directory:

<gene_id>_density_plot.pdf
<gene_id>_density_plot.png

The x-axis is nucleotide position relative to the selected transcript region, and the y-axis shows normalized density used by the plotting function.

Examples¶

Draw the density profile of one gene:

rpf_Geneplot \
  -r RIBO_merged.txt \
  -g AT1G01010

Draw one profile for each gene in a list:

rpf_Geneplot \
  -r RIBO_merged.txt \
  -l target_gene_ids.txt

Use log2 scaling on the y-axis:

rpf_Geneplot \
  -r RIBO_merged.txt \
  -g AT1G01010 \
  --log 2

Use log10 scaling on the y-axis:

rpf_Geneplot \
  -r RIBO_merged.txt \
  -l target_gene_ids.txt \
  --log 10

Notes¶

The command does not take an output prefix; plot file names are generated from gene/transcript IDs.
The previous example using -b should be replaced by -r, which is the actual input-density argument.
If a gene/transcript ID is not found in the input table, the command reports it and skips that record.
Very long genes or many samples can generate large figures. Run the command on a small gene list first when checking a new dataset.