fix karyotype plot
tforest
parent
017bf2c4ed
commit
0425fcfa03
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@ -152,12 +152,24 @@ def plot_matrix(mat, legend=None, color_scale_type="YlGn", cbarlabel = "qt", tit
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plt.show()
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plt.show()
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def plot(x, y, outfile = None, outfolder = None, ylab=None, xlab=None,
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def plot(x, y, outfile = None, outfolder = None, ylab=None, xlab=None,
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title=None, label = None, show=True):
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title=None, label = None, show=True, nb_subplots = None, subplot_init = False,
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subplot_id = None):
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if subplot_init:
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# define a certain amount of subplots
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fig, axs = plt.subplots(nb_subplots)
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if x:
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if x:
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fig, = plt.plot(x, y)
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if nb_subplots:
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axs[subplot_id].plot(x, y)
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else:
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fig, = plt.plot(x, y)
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else:
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else:
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# x is optional
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# x is optional
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fig, = plt.plot(y)
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if nb_subplots:
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# define a certain amount of subplots
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axs[subplot_id].plot(y)
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else:
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fig, = plt.plot(y)
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if label:
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if label:
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# if legend
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# if legend
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fig.set_label(label)
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fig.set_label(label)
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@ -195,37 +207,69 @@ def barplot(x, y, ylab=None, xlab=None, title=None):
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plt.show()
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plt.show()
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def plot_chrom_continuity(vcf_entries, chr_id, x=None, y=None, outfile = None,
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def plot_chrom_continuity(vcf_entries, chr_id, x=None, y=None, outfile = None,
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outfolder = None, returned=False, show=True, label=True):
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outfolder = None, returned=False, show=True, label=True, step=1, nb_subplots = None,
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subplot_init = False, subplot_id = None, title = None):
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chr_name = list(vcf_entries.keys())[chr_id]
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chr_name = list(vcf_entries.keys())[chr_id]
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if label:
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if label:
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label = chr_name
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label = chr_name
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if not title:
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title = "Genotyped pos in chr "+str(chr_id+1)+":'"+chr_name+"'"
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chr_entries = vcf_entries[chr_name]
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chr_entries = vcf_entries[chr_name]
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genotyped_pos = vcf_utils.genotyping_continuity_plot(chr_entries)
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genotyped_pos = vcf_utils.genotyping_continuity_plot(chr_entries, step=step)
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if returned:
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if returned:
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# if we do not want to plot while executing
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# if we do not want to plot while executing
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# useful for storing the x,y coords in a variable for ex.
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# useful for storing the x,y coords in a variable for ex.
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return genotyped_pos
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return genotyped_pos
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else:
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else:
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# to plot on the fly
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# to plot on the fly
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plot(x, y=genotyped_pos[1], ylab = "genotyped pos.",
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plot(x=genotyped_pos[0], y=genotyped_pos[1], ylab = "genotyped pos.",
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xlab = "pos. in ref.",
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xlab = "pos. in ref.",
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title = "Genotyped pos in chr "+str(chr_id+1)+":'"+chr_name+"'",
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title = title,
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outfile = outfile, outfolder = outfolder, show=show, label=label)
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outfile = outfile, outfolder = outfolder, show=show, label=label,
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nb_subplots = nb_subplots, subplot_init = subplot_init, subplot_id = subplot_id)
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def plot_whole_karyotype(recent_variants, mem_clean = False):
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def plot_whole_karyotype(recent_variants, mem_clean = False, step = 1, show = True, min_chr_id = 0,
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max_chr_id = None, stacked = False, title = None):
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coords = []
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coords = []
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for chr in range(len(recent_variants)):
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if max_chr_id :
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x, y = vcf_utils.customgraphics.plot_chrom_continuity(recent_variants, chr_id = chr, show = False, returned = True)
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nb_iter = max_chr_id
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coords.append([x, y])
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else:
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if mem_clean:
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nb_iter = len(recent_variants)
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start = time.time()
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if show :
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del x
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iter_start = min_chr_id + 1
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del y
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if not step :
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gc.collect()
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step = round(len(recent_variants[list(recent_variants.keys())[min_chr_id]]) / step)
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end = time.time()
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if stacked:
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print("Cleaned mem. in", str(datetime.timedelta(seconds=end - start)))
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nb_subplots = nb_iter - min_chr_id
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subplot_init = True
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else:
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nb_subplots = None
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subplot_init = False
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vcf_utils.customgraphics.plot_chrom_continuity(recent_variants, chr_id = min_chr_id, show = False, returned = False, step = step,
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nb_subplots = nb_subplots, subplot_init = subplot_init, subplot_id = min_chr_id)
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else :
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iter_start = 0
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for chr in range(iter_start, nb_iter):
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if show == False:
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x, y = vcf_utils.customgraphics.plot_chrom_continuity(recent_variants, chr_id = chr, show = False, returned = True, step = step)
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coords.append([x, y])
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if mem_clean:
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start = time.time()
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del x
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del y
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gc.collect()
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end = time.time()
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print("Cleaned mem. in", str(datetime.timedelta(seconds=end - start)))
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else:
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# if show is enable, use a step
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step = round(len(recent_variants[list(recent_variants.keys())[chr]]) / 1000)
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vcf_utils.customgraphics.plot_chrom_continuity(recent_variants, chr_id = chr, show = False, returned = False, step = step, subplot_id = chr)
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# last case
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if show == True:
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vcf_utils.customgraphics.plot_chrom_continuity(recent_variants, chr_id = nb_iter, show = True, returned = False, step = step, subplot_id = nb_iter, title = title)
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# maybe add a clean of recent_variants in extreme cases, before building the plots
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# maybe add a clean of recent_variants in extreme cases, before building the plots
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return coords
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if show == False:
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return coords
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def plot_chrom_coverage(vcf_entries, chr_id):
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def plot_chrom_coverage(vcf_entries, chr_id):
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chr_name = list(vcf_entries.keys())[chr_id]
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chr_name = list(vcf_entries.keys())[chr_id]
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10
vcf_utils.py
10
vcf_utils.py
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@ -170,21 +170,23 @@ def build_polymorph_coverage_matrix(entries, noGenotype, diploid=True, na_omit =
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mat = mat / row_sums[:, np.newaxis]
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mat = mat / row_sums[:, np.newaxis]
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return mat
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return mat
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def genotyping_continuity_plot(vcf_entries, verbose=False):
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def genotyping_continuity_plot(vcf_entries,
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verbose=False,
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step = 1):
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last_pos = int(sorted(list(vcf_entries.keys()))[-1])
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last_pos = int(sorted(list(vcf_entries.keys()))[-1])
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x = 0
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x = 0
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y = 1
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y = 1
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coords = [[], []]
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coords = [[], []]
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print(last_pos, "sites to scan")
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print(last_pos, "sites to scan")
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for k, pos in enumerate(range(last_pos)):
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for k, pos in enumerate(range(0, last_pos, step)):
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if verbose:
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if verbose:
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progress = round(k/int(last_pos))*100
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progress = round(k/int(last_pos))*100
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if progress % 10 == 0:
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if progress % 10 == 0:
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print(progress, "%")
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print(progress, "%")
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# if pos is genotyped
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# if pos is genotyped
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if k in vcf_entries:
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if k in vcf_entries:
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y+=1
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y+=1*step
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x+=1
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x+=1*step
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coords[0].append(x)
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coords[0].append(x)
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coords[1].append(y)
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coords[1].append(y)
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return coords
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return coords
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