gwaslab 3.4.46__py3-none-any.whl → 3.4.47__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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- gwaslab/g_version.py +7 -7
- gwaslab/io_to_formats.py +8 -3
- gwaslab/util_ex_calculate_ldmatrix.py +20 -7
- gwaslab/util_ex_calculate_prs.py +13 -7
- gwaslab/util_ex_process_ref.py +22 -11
- gwaslab/viz_aux_chromatin.py +4 -3
- gwaslab/viz_plot_mqqplot.py +80 -42
- gwaslab/viz_plot_regional2.py +792 -0
- gwaslab/viz_plot_stackedregional.py +62 -43
- {gwaslab-3.4.46.dist-info → gwaslab-3.4.47.dist-info}/METADATA +1 -1
- {gwaslab-3.4.46.dist-info → gwaslab-3.4.47.dist-info}/RECORD +15 -14
- {gwaslab-3.4.46.dist-info → gwaslab-3.4.47.dist-info}/WHEEL +1 -1
- {gwaslab-3.4.46.dist-info → gwaslab-3.4.47.dist-info}/LICENSE +0 -0
- {gwaslab-3.4.46.dist-info → gwaslab-3.4.47.dist-info}/LICENSE_before_v3.4.39 +0 -0
- {gwaslab-3.4.46.dist-info → gwaslab-3.4.47.dist-info}/top_level.txt +0 -0
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@@ -58,6 +58,8 @@ def plot_stacked_mqq(objects,
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region_hspace=0.05,
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subplot_height=4,
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region_lead_grid_line=None,
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fontsize=9,
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font_family="Arial",
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build="99",
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save=None,
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save_args=None,
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@@ -83,6 +85,11 @@ def plot_stacked_mqq(objects,
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region_chromatin_height = len(region_chromatin_files) * region_chromatin_height
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if region_chromatin_labels is None:
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region_chromatin_labels = []
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if title_args is None:
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title_args = {"family":"Arial"}
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else:
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if "family" not in title_args.keys():
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title_args["family"] = "Arial"
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# create figure and axes ##################################################################################################################
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if mode=="r":
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if len(vcfs)==1:
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@@ -131,6 +138,7 @@ def plot_stacked_mqq(objects,
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##########################################################################################################################################
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# a dict to store lead variants of each plot
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lead_variants_is={}
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lead_variants_is_color ={}
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##########################################################################################################################################
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# plot manhattan plot
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@@ -144,7 +152,7 @@ def plot_stacked_mqq(objects,
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#################################################################
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if index==0:
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# plot last m and gene track
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fig,log,
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fig,log,lead_snp_is,lead_snp_is_color = mqqplot(sumstats,
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chrom="CHR",
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pos="POS",
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p="P",
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snpid="SNPID",
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vcf_path=vcfs[index],
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mode=mode,
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fontsize=fontsize,
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font_family=font_family,
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region_lead_grid=False,
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gtf_path="default",
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rr_ylabel=False,
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log=log,
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**mqq_args_for_each_plot[index]
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)
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lead_variants_is[index] =
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lead_variants_is[index] = lead_snp_is
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lead_variants_is_color[index] = lead_snp_is_color
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else:
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# plot only the scatter plot
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fig,log,
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fig,log,lead_snp_is,lead_snp_is_color = mqqplot(sumstats,
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chrom="CHR",
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pos="POS",
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p="P",
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@@ -177,6 +188,8 @@ def plot_stacked_mqq(objects,
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snpid="SNPID",
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vcf_path=vcfs[index],
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region_lead_grid=False,
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fontsize=fontsize,
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font_family=font_family,
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mode=mode,
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rr_ylabel=False,
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region_ld_legend=False,
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@@ -190,8 +203,8 @@ def plot_stacked_mqq(objects,
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log=log,
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**mqq_args_for_each_plot[index]
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)
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lead_variants_is[index] =
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lead_variants_is[index] = lead_snp_is
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lead_variants_is_color[index] = lead_snp_is_color
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if len(region_chromatin_files)>0 and mode=="r":
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xlim_i = axes[-1].get_xlim()
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fig = _plot_chromatin_state( region_chromatin_files = region_chromatin_files,
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ax = axes[-2],
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xlim_i=xlim_i,
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log=log,
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verbose=verbose
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verbose=verbose,
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fontsize = fontsize,
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font_family = font_family)
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# adjust labels
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# drop labels for each plot
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# set a common laebl for all plots
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@@ -210,44 +225,44 @@ def plot_stacked_mqq(objects,
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# title_box = dict(boxstyle='square', facecolor='white', alpha=1.0, edgecolor="black")
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# title_box = {}
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if titles is not None and mode=="r":
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else:
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#if title_args is None:
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# title_args = {}
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#if titles is not None and mode=="r":
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# if title_pos is None:
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# title_pos = [0.01,0.99]
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# for index,title in enumerate(titles):
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#
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# current_text = axes[index].text(title_pos[0], title_pos[1] , title, transform=axes[index].transAxes,ha="left", va='top',zorder=999999, **title_args)
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# r = fig.canvas.get_renderer()
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# bb = current_text.get_window_extent(renderer=r).transformed(axes[index].transAxes.inverted())
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# width = bb.width
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# height = bb.height
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#
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# rect = patches.Rectangle((0.0,1.0 - height),
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# height=height + 0.02*2,
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# width=width + 0.01*2,
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# transform=axes[index].transAxes,
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# linewidth=1,
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# edgecolor='black',
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# facecolor='white',
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# alpha=1.0,
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# zorder=99998)
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# axes[index].add_patch(rect)
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# rect.set(zorder=99998)
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#else:
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if title_pos is None:
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title_pos = [0.01,0.97]
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for index,title in enumerate(titles):
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axes[index].text(title_pos[0], title_pos[1] , title, transform=axes[index].transAxes,ha="left", va='top',zorder=999999, **title_args)
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##########################################################################################################################################
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# draw the line for lead variants
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_draw_grid_line_for_lead_variants(mode, lead_variants_is, n_plot, axes, region_lead_grid_line,region_chromatin_files)
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_draw_grid_line_for_lead_variants(mode, lead_variants_is,lead_variants_is_color, n_plot, axes, region_lead_grid_line,region_chromatin_files)
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##########################################################################################################################################
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_drop_old_y_labels(axes, n_plot)
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_add_new_y_label(mode, fig, gene_track_height,n_plot,subplot_height )
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_add_new_y_label(mode, fig, gene_track_height,n_plot,subplot_height ,fontsize,font_family)
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##########################################################################################################################################
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save_figure(fig = fig, save = save, keyword= "stacked_" + mode, save_args=save_args, log = log, verbose=verbose)
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for index in range(n_plot):
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axes[index].set_ylabel("")
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def _draw_grid_line_for_lead_variants(mode, lead_variants_is, n_plot, axes, region_lead_grid_line,region_chromatin_files):
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def _draw_grid_line_for_lead_variants(mode, lead_variants_is,lead_variants_is_color, n_plot, axes, region_lead_grid_line,region_chromatin_files):
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if len(region_chromatin_files)>0:
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n_plot_and_track = n_plot+2
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else:
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n_plot_and_track = n_plot+1
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if mode=="r":
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for index, sig_is in lead_variants_is.items():
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for sig_i in sig_is:
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for j, sig_i in enumerate(sig_is):
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try:
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region_lead_grid_line["color"]=lead_variants_is_color[index][j]
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except:
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pass
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if sig_i is not None:
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for each_axis_index in range(n_plot_and_track):
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axes[each_axis_index].axvline(x=sig_i, zorder=2,**region_lead_grid_line)
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def _add_new_y_label(mode, fig, gene_track_height,n_plot,subplot_height ):
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def _add_new_y_label(mode, fig, gene_track_height,n_plot,subplot_height ,fontsize,font_family):
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gene_track_height_ratio = gene_track_height/(gene_track_height + n_plot*subplot_height)
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ylabel_height = (1 - gene_track_height_ratio)*0.5 + gene_track_height_ratio
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if mode=="r":
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fig.text(0.08, ylabel_height , "$-log_{10}(P)$", va='center', rotation='vertical')
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fig.text(0.93, ylabel_height, "Recombination rate(cM/Mb)", va='center', rotation=-90)
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fig.text(0.08, ylabel_height , "$-log_{10}(P)$", va='center', rotation='vertical',fontsize=fontsize,family=font_family)
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fig.text(0.93, ylabel_height, "Recombination rate(cM/Mb)", va='center', rotation=-90,fontsize=fontsize,family=font_family)
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elif mode=="m":
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fig.text(0.08, ylabel_height , "$-log_{10}(P)$", va='center', rotation='vertical')
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fig.text(0.08, ylabel_height , "$-log_{10}(P)$", va='center', rotation='vertical',fontsize=fontsize,family=font_family)
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def _sort_args(mqq_args, n_plot):
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mqq_args_for_each_plot={i:{} for i in range(n_plot)}
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@@ -12,14 +12,14 @@ gwaslab/g_SumstatsT.py,sha256=u_DighLMnMxwTLnqm-B58pA0G6WXRj6pudPyKMVKjSU,2133
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gwaslab/g_Sumstats_summary.py,sha256=FECvvFXJVKaCX5dggBvvk9YvJ6AbdbcLfjltysX7wEE,6380
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gwaslab/g_meta.py,sha256=htWlgURWclm9R6UqFcX1a93WN27xny7lGUeyJZOtszQ,2583
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gwaslab/g_vchange_status.py,sha256=jLoVzMJFhB5k_cJKzHuBNc2HZGBWydAunCNa0n_d54g,1923
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gwaslab/g_version.py,sha256=
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gwaslab/g_version.py,sha256=_mujOAftzn4ic9p92turA93xxg-RqxoWIqVfJLiNaSg,1886
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gwaslab/hm_casting.py,sha256=FqP4EQl83Q2OKLw004OgLIvUH795TVCGwziLk5jsHqY,11368
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gwaslab/hm_harmonize_sumstats.py,sha256=1hjUdle2DSKHGBp2BktfFqf-QHU_q2xWl_mPhiYc_ZA,78616
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gwaslab/hm_rsid_to_chrpos.py,sha256=ODWREO0jPN0RAfNzL5fRzSRANfhiksOvUVPuEsFZQqA,6552
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gwaslab/io_preformat_input.py,sha256=AZ43WGqVTzbo3XtClWhjRjsj6pBR9stw6JBL_TZ461U,20673
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gwaslab/io_read_ldsc.py,sha256=8S9n4imgl4d0WPms_GYld-6uUM5z7iWGiCA-M814kzY,12123
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gwaslab/io_read_tabular.py,sha256=EG-C6KhCutt4J4LlOMgXnqzJvU-EZXzVhMvaDFnHrMM,2380
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gwaslab/io_to_formats.py,sha256=
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gwaslab/io_to_formats.py,sha256=m57dGoqmHzAE1E27j9YxYKVCA12_lKd1qCnZtp0WZLw,29401
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gwaslab/io_to_pickle.py,sha256=HhePU0VcaGni0HTNU0BqoRaOnrr0NOxotgY6ISdx3Ck,1833
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gwaslab/ldsc_irwls.py,sha256=83JbAMAhD0KOfpv4IJa6LgUDfQjp4XSJveTjnhCBJYQ,6142
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gwaslab/ldsc_jackknife.py,sha256=XrWHoKS_Xn9StG1I83S2vUMTertsb-GH-_gOFYUhLeU,17715
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@@ -30,14 +30,14 @@ gwaslab/ldsc_sumstats.py,sha256=O0olsDxKlh1MJ1gAuEN1t40rxhajOEwOQ20ak7xoDrI,2624
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gwaslab/qc_check_datatype.py,sha256=kW68uk4dTLOU2b1dHoVat6n0loundDysAjIqxsXW28Q,3379
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gwaslab/qc_fix_sumstats.py,sha256=-DQz5dPW6YXXVP-LV2Txa4lJrpZHhqAoKNny6IYAW18,93100
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gwaslab/run_script.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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gwaslab/util_ex_calculate_ldmatrix.py,sha256=
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gwaslab/util_ex_calculate_prs.py,sha256=
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gwaslab/util_ex_calculate_ldmatrix.py,sha256=Z_spxbq6SHDS0v84I59YTTF40iyLQIOZbt0dmEcNJjw,15417
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gwaslab/util_ex_calculate_prs.py,sha256=9uJ588Sdj4V0vw3OZ9NeLECwOvW67f0IdLandVPS5RY,9442
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gwaslab/util_ex_gwascatalog.py,sha256=--Gde9HrsikfYTeFqSaYz0gUODr9wmv_gV6GZGNlElg,7688
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gwaslab/util_ex_ldproxyfinder.py,sha256=wWNW9wITWozj23gT41LR00WxU-rrHpGKbxs2H_3jEyM,9431
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gwaslab/util_ex_ldsc.py,sha256=a-OwyWmDcyinTPRfCNSeNYm6beVsydFeYmRAXAPcRnI,18350
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gwaslab/util_ex_plink_filter.py,sha256=pK1Yxtv9-J4rMOdVAG7VU9PktvI6-y4FxBiVEH0QuRs,1673
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gwaslab/util_ex_process_h5.py,sha256=ynFvo3zxgvOxWYL565v2IQf8P6iEuq7UlKQ_ULxrd6Y,2831
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gwaslab/util_ex_process_ref.py,sha256=
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gwaslab/util_ex_process_ref.py,sha256=GQ0ZEWLxGpHLdBs3tqnAqKn3Pqx1A1YvNbYrBLBvXeg,17126
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gwaslab/util_ex_run_2samplemr.py,sha256=5c0DGF694T9j0Y58L2I7pr1_Z1hfpaatIgix7P5oPA8,9127
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gwaslab/util_ex_run_clumping.py,sha256=Y8KeUKuSpGc1a8iI_VKUgVQpAVBd7O9F11p85jY4oW4,7868
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gwaslab/util_ex_run_coloc.py,sha256=u57h8wPbTCOf6aY5u5DpzK1gv7inuDT8a15UGo-1ras,6288
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@@ -53,7 +53,7 @@ gwaslab/util_in_get_sig.py,sha256=9kq1GXacknO2YnVmsTli1GlPA728ASweTZ3UKm3Wszo,38
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gwaslab/util_in_meta.py,sha256=5K9lIZcIgUy0AERqHy1GvMN2X6dp45JUUgopuDLgt4o,11284
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gwaslab/util_in_snphwe.py,sha256=-KpIDx6vn_nah6H55IkV2OyjXQVXV13XyBL069WE1wM,1751
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gwaslab/viz_aux_annotate_plot.py,sha256=R-1GT89E4NEBAMNTYzNawdi9rjQV5LCnODgnYOOKsys,32184
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gwaslab/viz_aux_chromatin.py,sha256=
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gwaslab/viz_aux_chromatin.py,sha256=7cGmej5EkKO7fxR1b5w8r1oRRl9ofVzFRG52SCYWtz0,4109
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gwaslab/viz_aux_quickfix.py,sha256=Z6ZNEAUFuWVDTzH-qGreNGxPxJLCmqhXtBrvDOgo4g8,18308
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gwaslab/viz_aux_reposition_text.py,sha256=iRIP-Rkltlei068HekJcVubiqPrunBqvAoSQ1eHk04M,4304
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gwaslab/viz_aux_save_figure.py,sha256=nL-aoE8Kg06h7FgleGRBIZjhI-6w5gpn3E1HWMwBig8,2664
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@@ -62,11 +62,12 @@ gwaslab/viz_plot_compare_effect.py,sha256=iA74jMzh-G65U6BeXyQro08tPlJWpNyvtrjFsY
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gwaslab/viz_plot_forestplot.py,sha256=xgOnefh737CgdQxu5naVyRNBX1NQXPFKzf51fbh6afs,6771
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gwaslab/viz_plot_miamiplot.py,sha256=rCFEp7VNuVqeBBG3WRkmFAtFklbF79BvIQQYiSY70VY,31238
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gwaslab/viz_plot_miamiplot2.py,sha256=SWv82D8UBbREKsk8EoKth-2w68l6FbXyVLsb_E1hh8o,15882
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gwaslab/viz_plot_mqqplot.py,sha256=
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gwaslab/viz_plot_mqqplot.py,sha256=udOTBKSX239KLFNauhHGDJHp0Viu18NkGwFn5GtAHuM,63297
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gwaslab/viz_plot_qqplot.py,sha256=psQgVpP29686CEZkzQz0iRbApzqy7aE3GGiBcazVvNw,7247
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gwaslab/viz_plot_regional2.py,sha256=6Dfbq5vFm5B63nLUpaTrlq96x4CruIgJu0TXXq3a_Ck,34546
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gwaslab/viz_plot_regionalplot.py,sha256=8u-5-yfy-UaXhaxVVz3Y5k2kBAoqzczUw1hyyD450iI,37983
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gwaslab/viz_plot_rg_heatmap.py,sha256=PidUsgOiEVt6MfBPCF3_yDhOEytZ-I1q-ZD6_0pFrV4,13713
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gwaslab/viz_plot_stackedregional.py,sha256=
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gwaslab/viz_plot_stackedregional.py,sha256=HISwtPDV84mT3PS41e2sXq77GPBujgSKVX1mQ4bEeKs,15820
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gwaslab/viz_plot_trumpetplot.py,sha256=ZHdc6WcVx0-oKoj88yglRkmB4bS9pOiEMcuwKW35Yvo,42672
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gwaslab/data/formatbook.json,sha256=N2nJs80HH98Rsu9FxaSvIQO9J5yIV97WEtAKjRqYwiY,38207
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gwaslab/data/reference.json,sha256=k8AvvgDsuLxzv-NCJHWvTUZ5q_DLAFxs1Th3jtL313k,11441
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gwaslab/data/hapmap3_SNPs/hapmap3_db151_hg38.snplist.gz,sha256=Y8ZT2FIAhbhlgCJdE9qQVAiwnV_fcsPt72usBa7RSBM,10225828
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gwaslab/data/high_ld/high_ld_hla_hg19.bed.gz,sha256=R7IkssKu0L4WwkU9SrS84xCMdrkkKL0gnTNO_OKbG0Y,219
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gwaslab/data/high_ld/high_ld_hla_hg38.bed.gz,sha256=76CIU0pibDJ72Y6UY-TbIKE9gEPwTELAaIbCXyjm80Q,470
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gwaslab-3.4.
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gwaslab-3.4.
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gwaslab-3.4.47.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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gwaslab-3.4.47.dist-info/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
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gwaslab-3.4.47.dist-info/METADATA,sha256=G_RLrYWZe0z6Wbvyl_g7rXnJKoZ6HFKUHM66ogtfyug,7765
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gwaslab-3.4.47.dist-info/WHEEL,sha256=y4mX-SOX4fYIkonsAGA5N0Oy-8_gI4FXw5HNI1xqvWg,91
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gwaslab-3.4.47.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
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gwaslab-3.4.47.dist-info/RECORD,,
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