FragMapper

Maintained by Seth Veenbaas

import rnavigate as rnav

Import data to RNAvigate and run Fragmapper analysis

from rnavigate.examples import quinaxoline, linezolid, methyl

The above import statement is equivalent to running the following code from inside /path/to/RNAvigate/rnavigate/examples/rrna_fragmap/.

# Reference structure data is shared between samples
common_data = rnav.Sample(
    sample='6HA1 - LSU',
    sequence='6HA1_LSU.fasta',
    pdb={'pdb': '6HA1_LSU.pdb',
         'sequence': 'sequence',
         'chain': 'A'},
    ss='6HA1_LSU.json'
)
# Flip structure diagram along x and y axes
common_data.data['ss'].data["X_coordinate"] *= -1
common_data.data['ss'].data["Y_coordinate"] *= -1
# Quinaxoline test sample
quinoxiline = rnav.Sample(
    'B. sub rRNA FragMaP: quinoxiline',
    inherit=common_data,
    shapemap='2_QN_DMSO_subtracted_LSU_profile.txt'
)
# Linezolid test sample
lnz = rnav.Sample(
    'B. sub rRNA FragMaP: linezolid',
    inherit=common_data,
    shapemap='2_ZLD_DMSO_subtracted_LSU_profile.txt'
)
# Methyl control sample
met = rnav.Sample(
    'B. sub rRNA FragMaP: methyl',
    inherit=common_data,
    shapemap='2_Methyl_DMSO_subtracted_LSU_profile.txt'
)

# Run Fragmapper analysis and saving a FragMaP profile object
# NOTE: Fragmapper requires 1 test sample and 1 control sample
qn_fm = rnav.analysis.Fragmapper(quinaxoline, methyl)
lnz_fm = rnav.analysis.Fragmapper(linezolid, methyl)

FragMaP scatter plots

Scatter plot with FragMaP profiles

# FragMapper.plot_scatter()
print(lnz_fm.get_data("fragmap").data.columns)
fig, ax = lnz_fm.plot_scatter()
fig, ax = qn_fm.plot_scatter()

Scatter plot with raw mutation rates

# FragMaP_profile_object.plot_scatter()
fig1, ax1 = lnz_fm.plot_scatter()
fig2, ax2 = qn_fm.plot_scatter()

View FragMaP profile

plot = rnav.plot_profile(
    samples=[lnz_fm],
    profile="fragmap",
    region=[2000, 2700],
    sequence='shapemap',
    plot_error=False
    )
ax = plot.axes[0, 0]
ax.set(ylim=[-2, 10])
ax.legend(['ZLD FragMaP Profile']);

View raw sample data

plot = rnav.plot_skyline(
    samples=[lnz_fm],
    profile="fragmap",
    columns=["Modified_rate_1", "Modified_rate_2", "Delta_rate"],
    sequence="shapemap",
    region=[2000, 2700],
    annotations=["fragmap_sites"],
    annotations_mode='bar',
    plot_kwargs={"subplot_kw": {"ylim": (-0.01, 0.2)}},
    )

plot.axes[0, 0].legend(
    ["ZLD mutation rate", "methyl mutation rate", "delta rate"]
    );

View FragMaP site annotation in secondary structure

with rnav.styles.Settings({'ss': {'structure': {'linewidth': 2}}}):
    plot = rnav.plot_ss(
        [lnz_fm],
        profile='fragmap',
        structure='ss',
        colors={'structure': 'sequence',
                'nucleotides': 'none',},
        bp_style='conventional',
        annotations=['fragmap_sites'],
        nt_ticks=100
        )