plot_diagnostic | R Documentation |
This function generates diagnostic plots: RPF density at the start codon; RPF density at the stop codon; histogram of RPF lengths; heatmap of RPF counts by RPF length and frame
Input '.bam' file must contain 'tag.ZW' of posterior weights computed from 'RSEM'
plot_diagnostic( bam_fname, transcript_length_fname, plot_title = "", start_min = -20, start_max = 5, stop_min = -5, stop_max = 20, length_min = 15, length_max = 35 )
bam_fname |
character; file path to .bam alignment file |
transcript_length_fname |
character; file path to transcriptome lengths file |
plot_title |
character; title for diagnostic plot |
start_min |
integer; 5'-most position to include in plot, relative to start codon |
start_max |
integer; 3'-most position to include in plot, relative to start codon |
stop_min |
integer; 5'-most position to include in plot, relative to stop codon |
stop_max |
integer; 3'-most position to include in plot, relative to stop codon |
length_min |
integer; minimum RPF length |
length_max |
integer; maximum RPF length |
A patchwork object of diagnostic plots
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