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v2.0.33 plot updates
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allele plot sgRNAs that extend beyond plot are
marked quantification window shading and right-side correction version
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@kclem
kclem committed Apr 3, 2020
1 parent 90e677f commit a66c402
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Showing 3 changed files with 30 additions and 14 deletions.
23 changes: 12 additions & 11 deletions CRISPResso2/CRISPRessoCORE.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2607,14 +2607,15 @@ def count_alternate_alleles(sub_base_vectors,ref_name,ref_sequence,ref_total_aln
if include_idxs_list[idx] == lastIdx + 1:
lastIdx = include_idxs_list[idx]
else:
p = matplotlib.patches.Rectangle((lastStart-0.5, 0), 1+(lastIdx-lastStart)-0.5, y_max,fill=None,edgecolor=(0,0,0,0.25),linestyle=(0,(5,2)),linewidth=2)
p = matplotlib.patches.Rectangle((lastStart-0.5, 0), 1+(lastIdx-lastStart), y_max,facecolor=(0,0,0,0.05),edgecolor=(0,0,0,0.25),linestyle=(0,(5,2)),linewidth=2)
plt.gca().add_patch(p) #gca = get current axis
lastStart = include_idxs_list[idx]
lastIdx = include_idxs_list[idx]
p = matplotlib.patches.Rectangle((lastStart-0.5, 0), 1+(lastIdx-lastStart)-0.5, y_max,fill=None,edgecolor=(0,0,0,0.25),linestyle=(0,(5,2)),linewidth=2,label='Quantification window')
p = matplotlib.patches.Rectangle((lastStart-0.5, 0), 1+(lastIdx-lastStart), y_max,facecolor=(0,0,0,0.05),edgecolor=(0,0,0,0.25),linestyle=(0,(5,2)),linewidth=2,label='Quantification window')
plt.gca().add_patch(p)

plt.plot(all_indelsub_count_vectors[ref_name],'r',lw=3,label=get_plot_title_with_ref_name('Combined Insertions/Deletions/Substitutions',ref_name))
# plt.plot(all_indelsub_count_vectors[ref_name],marker='o')
#plt.hold(True)

if cut_points:
Expand Down Expand Up @@ -2669,11 +2670,11 @@ def count_alternate_alleles(sub_base_vectors,ref_name,ref_sequence,ref_total_aln
if include_idxs_list[idx] == lastIdx + 1:
lastIdx = include_idxs_list[idx]
else:
p = matplotlib.patches.Rectangle((lastStart-0.5, 0), 1+(lastIdx-lastStart)-0.5, y_max,fill=None,edgecolor=(0,0,0,0.25),linestyle=(0,(5,2)),linewidth=2)
p = matplotlib.patches.Rectangle((lastStart-0.5, 0), 1+(lastIdx-lastStart), y_max,facecolor=(0,0,0,0.05),edgecolor=(0,0,0,0.25),linestyle=(0,(5,2)),linewidth=2)
plt.gca().add_patch(p) #gca = get current axis
lastStart = include_idxs_list[idx]
lastIdx = include_idxs_list[idx]
p = matplotlib.patches.Rectangle((lastStart-0.5, 0), 1+(lastIdx-lastStart)-0.5, y_max,fill=None,edgecolor=(0,0,0,0.25),linestyle=(0,(5,2)),linewidth=2,label='Quantification window')
p = matplotlib.patches.Rectangle((lastStart-0.5, 0), 1+(lastIdx-lastStart), y_max,facecolor=(0,0,0,0.05),edgecolor=(0,0,0,0.25),linestyle=(0,(5,2)),linewidth=2,label='Quantification window')
plt.gca().add_patch(p)

plt.plot(all_insertion_count_vectors[ref_name],'r',lw=3,label='Insertions')
Expand Down Expand Up @@ -2739,11 +2740,11 @@ def count_alternate_alleles(sub_base_vectors,ref_name,ref_sequence,ref_total_aln
if include_idxs_list[idx] == lastIdx + 1:
lastIdx = include_idxs_list[idx]
else:
p = matplotlib.patches.Rectangle((lastStart -0.5, 0), 1+(lastIdx-lastStart)-0.5, y_max,fill=None,edgecolor=(0,0,0,0.25),linestyle=(0,(5,2)),linewidth=2)
p = matplotlib.patches.Rectangle((lastStart -0.5, 0), 1+(lastIdx-lastStart), y_max,facecolor=(0,0,0,0.05),edgecolor=(0,0,0,0.25),linestyle=(0,(5,2)),linewidth=2)
plt.gca().add_patch(p) #gca = get current axis
lastStart = include_idxs_list[idx]
lastIdx = include_idxs_list[idx]
p = matplotlib.patches.Rectangle((lastStart -0.5, 0), 1+(lastIdx-lastStart)-0.5, y_max,fill=None,edgecolor=(0,0,0,0.25),linestyle=(0,(5,2)),linewidth=2,label='Quantification window')
p = matplotlib.patches.Rectangle((lastStart -0.5, 0), 1+(lastIdx-lastStart), y_max,facecolor=(0,0,0,0.05),edgecolor=(0,0,0,0.25),linestyle=(0,(5,2)),linewidth=2,label='Quantification window')
plt.gca().add_patch(p)


Expand Down Expand Up @@ -2886,11 +2887,11 @@ def count_alternate_alleles(sub_base_vectors,ref_name,ref_sequence,ref_total_aln
if include_idxs_list[idx] == lastIdx + 1:
lastIdx = include_idxs_list[idx]
else:
p = matplotlib.patches.Rectangle((lastStart-0.5, 0), 1+(lastIdx-lastStart)-0.5, y_max,fill=None,edgecolor=(0,0,0,0.25),linestyle=(0,(5,2)),linewidth=2)
p = matplotlib.patches.Rectangle((lastStart-0.5, 0), 1+(lastIdx-lastStart), y_max,facecolor=(0,0,0,0.05),edgecolor=(0,0,0,0.25),linestyle=(0,(5,2)),linewidth=2)
plt.gca().add_patch(p) #gca = get current axis
lastStart = include_idxs_list[idx]
lastIdx = include_idxs_list[idx]
p = matplotlib.patches.Rectangle((lastStart-0.5, 0), 1+(lastIdx-lastStart)-0.5, y_max,fill=None,edgecolor=(0,0,0,0.25),linestyle=(0,(5,2)),linewidth=2,label='Quantification window')
p = matplotlib.patches.Rectangle((lastStart-0.5, 0), 1+(lastIdx-lastStart), y_max,facecolor=(0,0,0,0.05),edgecolor=(0,0,0,0.25),linestyle=(0,(5,2)),linewidth=2,label='Quantification window')
plt.gca().add_patch(p)

if ref1_cut_points:
Expand Down Expand Up @@ -3123,11 +3124,11 @@ def count_alternate_alleles(sub_base_vectors,ref_name,ref_sequence,ref_total_aln
if include_idxs_list[idx] == lastIdx + 1:
lastIdx = include_idxs_list[idx]
else:
p = matplotlib.patches.Rectangle((lastStart-0.5, 0), 1+(lastIdx-lastStart)-0.5, y_max,fill=None,edgecolor=(0,0,0,0.25),linestyle=(0,(5,2)),linewidth=2)
p = matplotlib.patches.Rectangle((lastStart-0.5, 0), 1+(lastIdx-lastStart), y_max,facecolor=(0,0,0,0.05),edgecolor=(0,0,0,0.25),linestyle=(0,(5,2)),linewidth=2)
plt.gca().add_patch(p) #gca = get current axis
lastStart = include_idxs_list[idx]
lastIdx = include_idxs_list[idx]
p = matplotlib.patches.Rectangle((lastStart-0.5, 0), 1+(lastIdx-lastStart)-0.5, y_max,fill=None,edgecolor=(0,0,0,0.25),linestyle=(0,(5,2)),linewidth=2,label='Quantification window')
p = matplotlib.patches.Rectangle((lastStart-0.5, 0), 1+(lastIdx-lastStart), y_max,facecolor=(0,0,0,0.05),edgecolor=(0,0,0,0.25),linestyle=(0,(5,2)),linewidth=2,label='Quantification window')
plt.gca().add_patch(p)

if cut_points:
Expand Down Expand Up @@ -3271,7 +3272,7 @@ def count_alternate_alleles(sub_base_vectors,ref_name,ref_sequence,ref_total_aln
#adjust coordinates of sgRNAs
new_sel_cols_start = cut_point - plot_half_window
for (int_start,int_end) in refs[ref_name]['sgRNA_intervals']:
new_sgRNA_intervals += [(int_start - new_sel_cols_start,int_end - new_sel_cols_start)]
new_sgRNA_intervals += [(int_start - new_sel_cols_start - 1,int_end - new_sel_cols_start - 1)]

CRISPRessoPlot.plot_alleles_table(ref_seq_around_cut,df_alleles=df_to_plot,fig_filename_root=fig_filename_root,
MIN_FREQUENCY=args.min_frequency_alleles_around_cut_to_plot,MAX_N_ROWS=args.max_rows_alleles_around_cut_to_plot,SAVE_ALSO_PNG=save_png,base_editor_output=args.base_editor_output,sgRNA_intervals=new_sgRNA_intervals,sgRNA_names=sgRNA_names,sgRNA_mismatches=sgRNA_mismatches)
Expand Down
18 changes: 16 additions & 2 deletions CRISPResso2/CRISPRessoPlot.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -297,8 +297,9 @@ def add_sgRNA_to_ax(ax,sgRNA_intervals,sgRNA_y_start,sgRNA_y_height,amp_len,x_of
)

#if plot has trimmed the sgRNA, add a mark
if this_sgRNA_start != sgRNA_int[0]:
if (this_sgRNA_start) != sgRNA_int[0]:
ax.add_patch(
#patches.Rectangle((x_offset + 0.1+this_sgRNA_start, sgRNA_y_start), 0.1, sgRNA_y_height,facecolor='w',clip_on=clip_on)
patches.Rectangle((x_offset + 0.1+this_sgRNA_start, sgRNA_y_start), 0.1, sgRNA_y_height,facecolor='w',clip_on=clip_on)
)
if this_sgRNA_end != sgRNA_int[1]:
Expand Down Expand Up @@ -1096,6 +1097,19 @@ def plot_alleles_heatmap(reference_seq,fig_filename_root,X,annot,y_labels,insert
N_ROWS=len(X)
N_COLUMNS=plot_nuc_len

if N_ROWS < 1:
fig=plt.figure()
ax = fig.add_subplot(111)
plt.text(0.5, 0.5,'No Alleles',horizontalalignment='center',verticalalignment='center',transform = ax.transAxes)
txt.set_clip_on(False)

plt.savefig(fig_filename_root+'.pdf',bbox_inches='tight',bbox_extra_artists=(lgd,))
if SAVE_ALSO_PNG:
plt.savefig(fig_filename_root+'.png',bbox_inches='tight',bbox_extra_artists=(lgd,))
plt.close()
return


if sgRNA_intervals and len(sgRNA_intervals) > 0:
fig=plt.figure(figsize=(plot_nuc_len*0.3,(N_ROWS+2)*0.6))
gs1 = gridspec.GridSpec(N_ROWS+2,N_COLUMNS)
Expand All @@ -1120,7 +1134,7 @@ def plot_alleles_heatmap(reference_seq,fig_filename_root,X,annot,y_labels,insert
ax_hm.xaxis.set_ticks([])

if sgRNA_intervals and len(sgRNA_intervals) > 0:
add_sgRNA_to_ax(ax_hm_ref,sgRNA_intervals,sgRNA_y_start=-1,sgRNA_y_height=0.7,amp_len=plot_nuc_len,font_size='small',clip_on=False,sgRNA_names=sgRNA_names,sgRNA_mismatches=sgRNA_mismatches,x_offset=-1)
add_sgRNA_to_ax(ax_hm_ref,sgRNA_intervals,sgRNA_y_start=-1,sgRNA_y_height=0.7,amp_len=plot_nuc_len,font_size='small',clip_on=False,sgRNA_names=sgRNA_names,sgRNA_mismatches=sgRNA_mismatches,x_offset=0)

# todo -- add sgRNAs below reference plot
# if sgRNA_intervals:
Expand Down
3 changes: 2 additions & 1 deletion CRISPResso2/CRISPRessoShared.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@

import argparse
from collections import defaultdict
import errno
import gzip
import numpy as np
import os
Expand All @@ -30,7 +31,7 @@
else:
import cPickle as cp #python 2.7

__version__ = "2.0.32"
__version__ = "2.0.33"

###EXCEPTIONS############################
class FlashException(Exception):
Expand Down

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