Hello,
Congratulations on your package, it is so good! I just have some trouble with setting the annotation significance level in the Miami plot. I believe the function I am using is alright because at the end it does what I want, but I have tried sig_level, anno_sig_level and all the combinations of arguments I could found for plot_mqq and plot_miami2, it is stuck at 5E-08. I made a mockup point with P-value 1E-09 just to try that, indeed, it is able to label the annotations.
Is there a way of setting this that I am just missing?
I also have trouble setting up the colors of the significative line (sig_line), or lowering it to 1E-4 in the bottom plot, so I end up making additional lines. My command is the following:
Thank you for reading! Any suggestion or feedback is much appreciated
'''
gl.plot_miami2(path1=gwasres,
path2=magmares,
cols1=["SNPID", "P", "CHR", "POS"],
cols2=["SNPID", "P", "CHR", "POS"],
font_family="DejaVu Sans",
mode="m",
same_ylim=False,
skip1=2,
skip2=0.5,
region_hspace=0.08,
dpi=300,
#anotation
anno=True,
anno1="GENENAME",
anno2="SNPID_2",
sig_level_lead2=1e-4,
#Significative line up plot
sig_line1=False, # TODO: manage to set additional line at 5E-08 in red
#Suggestive line top plot
additional_line1=[1e-5],
additional_line_color1=["orange"],
#Significative line bottom plot
sig_line2=False,
additional_line2=[1e-4],
additional_line_color2=["red"],
verbose=True
)
'''
Hello,
Congratulations on your package, it is so good! I just have some trouble with setting the annotation significance level in the Miami plot. I believe the function I am using is alright because at the end it does what I want, but I have tried
sig_level,anno_sig_leveland all the combinations of arguments I could found for plot_mqq and plot_miami2, it is stuck at 5E-08. I made a mockup point with P-value 1E-09 just to try that, indeed, it is able to label the annotations.Is there a way of setting this that I am just missing?
I also have trouble setting up the colors of the significative line (sig_line), or lowering it to 1E-4 in the bottom plot, so I end up making additional lines. My command is the following:
Thank you for reading! Any suggestion or feedback is much appreciated
'''
gl.plot_miami2(path1=gwasres,
path2=magmares,
cols1=["SNPID", "P", "CHR", "POS"],
cols2=["SNPID", "P", "CHR", "POS"],
font_family="DejaVu Sans",
mode="m",
same_ylim=False,
skip1=2,
skip2=0.5,
region_hspace=0.08,
dpi=300,
#anotation
anno=True,
anno1="GENENAME",
anno2="SNPID_2",
sig_level_lead2=1e-4,
#Significative line up plot
sig_line1=False, # TODO: manage to set additional line at 5E-08 in red
#Suggestive line top plot
additional_line1=[1e-5],
additional_line_color1=["orange"],
#Significative line bottom plot
sig_line2=False,
additional_line2=[1e-4],
additional_line_color2=["red"],
verbose=True
)
'''