Sample QC metrics
An overview of quality control (QC) metrics for all samples, both before and after filtering. The QC metrics include:
no. of cells: Total number of barcodes called as cells for each sample.no. of UMIs: Sum of counts across all features for each cell with log-transformed values displayed.no. of genes: Number of unique features with non-zero counts for each cell with log-transformed values displayed.mito pct.: The proportion of reads that mapped to genes in the mitochondrial genome. High proportions are indicative of poor-quality cells (compromised membranes allow individual RNA molecules to escape while retaining mitochondria, leading to an increased relative abundance of mitochondrial transcript) or nuclei (incomplete removal of cytoplasm). Logit-transformed values are displayed as applying the logit (inverse logistic) transformation to mitochondrial proportions yields approximately Gaussian distributions.spliced pct.: The proportion of spliced reads. In single-nuclei RNA sequencing, high spliced proportions may indicate inadequate removal of cytoplasmic material from the nuclei. Logit-transformed values are displayed as applying the logit (inverse logistic) transformation to spliced proportions results in approximately Gaussian distributions.
suppressWarnings({
cat("### Pre-QC\n")
print(plot_qc_ranges_marginals(qc_dt, b_lvls, qc_names, qc_lu, cuts_dt, batch_var))
cat("\n\n")
cat("### After light QC\n")
print(plot_qc_ranges_marginals(kept_dt, b_lvls, qc_names, qc_lu, cuts_dt, batch_var))
cat("\n\n")
})Pre-QC
After light QC
QC metrics scatterplots
Pairwise relationships of QC metrics at individual cell level.
for (b in b_lvls) {
qc_tmp = qc_dt[ batch_var == b ]
if (nrow(qc_tmp) == 1)
next
cat('### ', b, '\n')
print(plot_qc_metric_scatter(qc_tmp, qc_names, qc_lu, cuts_dt[ batch_var == b ], b))
cat('\n\n')
}GSM5292146
GSM5292147
GSM5292156
GSM5292157
GSM5292158
GSM5292200
SRR27882183
SRR27882182
SRR27882181
SRR27882171
SRR27882170
SRR27882169
SRR27882094
SRR27882093
SRR27882092
SRR27882091
SRR27882090
SRR27882089
SRR27882088
SRR27882086
SRR27882085
SRR27882084
SRR27882158
SRR27882157
SRR27882156
SRR27882154
SRR27882153
SRR27882152
SRR27882151
SRR27882150
SRR27882149
SRR27882148
GSM5292143
GSM5292144
GSM5292145
GSM5292148
GSM5292149
GSM5292150
GSM5292151
GSM5292152
GSM5292153
GSM5292154
GSM5292155
GSM5292194
GSM5292195
GSM5292196
GSM5292197
GSM5292198
GSM5292199
SRR27882082
SRR27882081
SRR27882080
SRR27882079
SRR27882078
SRR27882077
SRR27882075
SRR27882074
SRR27882073
SRR27882180
SRR27882179
SRR27882178
SRR27882177
SRR27882175
SRR27882174
SRR27882173
SRR27882172
GSM5292174
GSM5292175
GSM5292176
GSM5292177
GSM5292178
GSM5292179
GSM5292180
GSM5292181
GSM5292182
GSM5292183
GSM5292184
GSM5292185
GSM5292186
GSM5292187
GSM5292188
GSM5292193
GSM5292201
SRR27882193
SRR27882192
SRR27882191
SRR27882190
SRR27882189
SRR27882188
SRR27882187
SRR27882186
SRR27882185
SRR27882165
SRR27882164
SRR27882163
SRR27882162
SRR27882161
SRR27882160
SRR27882159
GSM5292164
GSM5292169
GSM5292173
GSM5292190
GSM5292191
GSM5292192
GSM5292202
GSM5292203
GSM5292204
GSM5292205
GSM5292206
GSM5292207
GSM5292208
SRR27882214
SRR27882212
SRR27882203
SRR27882202
SRR27882201
SRR27882200
SRR27882199
SRR27882198
SRR27882197
SRR27882196
SRR27882194
GSM5292159
GSM5292160
GSM5292161
GSM5292162
GSM5292163
GSM5292165
GSM5292166
GSM5292167
GSM5292168
GSM5292170
GSM5292171
GSM5292172
GSM5292189
SRR27882168
SRR27882167
SRR27882166
SRR27882216
SRR27882215
SRR27882213
SRR27882211
SRR27882210
SRR27882209
SRR27882208
SRR27882207
SRR27882205
SRR27882204
How many cells and samples retained?
Table summarizing the number of cells before and after qc filtering. Some samples may have been excluded from further analysis due to insufficient number of cells.
calc_qc_summary(qc_dt, kept_dt, cuts_dt, qc_lu, batch_var) %>% knitr::kable()| sample_id | excluded | N pre-QC | N post-QC | N excluded | pct. excluded | pct. excluded by no. of UMIs | pct. excluded by no. of genes | pct. excluded by mito. pct. | pct. excluded by spliced pct. |
|---|---|---|---|---|---|---|---|---|---|
| SRR27882190 | FALSE | 10912 | 2929 | 7983 | 73.2 | 71.1 | 69.3 | 7.7 | 1.5 |
| GSM5292179 | FALSE | 2254 | 961 | 1293 | 57.4 | 25.0 | 24.4 | 50.9 | 2.5 |
| SRR27882203 | FALSE | 2729 | 1197 | 1532 | 56.1 | 14.0 | 17.0 | 47.1 | 2.7 |
| GSM5292169 | FALSE | 2973 | 1358 | 1615 | 54.3 | 35.2 | 33.1 | 48.3 | 0.3 |
| GSM5292195 | FALSE | 3655 | 1678 | 1977 | 54.1 | 14.0 | 12.9 | 47.3 | 5.4 |
| SRR27882162 | FALSE | 1384 | 715 | 669 | 48.3 | 5.6 | 7.6 | 45.4 | 1.4 |
| SRR27882168 | FALSE | 6587 | 3476 | 3111 | 47.2 | 13.2 | 13.6 | 42.0 | 0.6 |
| GSM5292204 | FALSE | 4374 | 2361 | 2013 | 46.0 | 4.0 | 4.0 | 44.5 | 0.5 |
| GSM5292206 | FALSE | 3361 | 2023 | 1338 | 39.8 | 23.4 | 18.2 | 21.9 | 1.5 |
| SRR27882197 | FALSE | 3717 | 2377 | 1340 | 36.1 | 17.0 | 15.4 | 24.9 | 0.9 |
| GSM5292182 | FALSE | 1843 | 1203 | 640 | 34.7 | 8.8 | 8.6 | 31.8 | 1.6 |
| GSM5292159 | FALSE | 5205 | 3558 | 1647 | 31.6 | 12.2 | 10.3 | 27.4 | 4.0 |
| GSM5292185 | FALSE | 4434 | 3109 | 1325 | 29.9 | 9.4 | 8.0 | 24.8 | 0.5 |
| GSM5292200 | FALSE | 6843 | 4813 | 2030 | 29.7 | 10.9 | 9.5 | 24.6 | 5.6 |
| SRR27882165 | FALSE | 8289 | 5898 | 2391 | 28.8 | 10.5 | 9.6 | 22.7 | 7.0 |
| GSM5292198 | FALSE | 7768 | 5645 | 2123 | 27.3 | 8.4 | 6.3 | 18.4 | 21.9 |
| SRR27882170 | FALSE | 8945 | 6577 | 2368 | 26.5 | 10.3 | 9.3 | 18.1 | 19.0 |
| GSM5292193 | FALSE | 6079 | 4480 | 1599 | 26.3 | 8.6 | 8.3 | 20.0 | 7.9 |
| GSM5292173 | FALSE | 3788 | 2795 | 993 | 26.2 | 12.9 | 11.4 | 18.7 | 0.4 |
| GSM5292190 | FALSE | 5413 | 4015 | 1398 | 25.8 | 10.3 | 9.5 | 19.1 | 1.8 |
| GSM5292189 | FALSE | 9446 | 7059 | 2387 | 25.3 | 15.9 | 12.8 | 8.7 | 12.2 |
| SRR27882183 | FALSE | 17079 | 12810 | 4269 | 25.0 | 24.3 | 19.3 | 1.3 | 0.2 |
| SRR27882200 | FALSE | 8994 | 6792 | 2202 | 24.5 | 7.0 | 7.2 | 20.1 | 0.2 |
| SRR27882160 | FALSE | 8908 | 6883 | 2025 | 22.7 | 10.6 | 8.9 | 15.6 | 1.1 |
| GSM5292196 | FALSE | 7221 | 5609 | 1612 | 22.3 | 10.4 | 7.4 | 13.5 | 11.5 |
| SRR27882192 | FALSE | 5120 | 4005 | 1115 | 21.8 | 8.1 | 8.8 | 16.6 | 1.8 |
| GSM5292161 | FALSE | 6486 | 5099 | 1387 | 21.4 | 7.8 | 7.0 | 16.9 | 3.6 |
| GSM5292192 | FALSE | 5053 | 4020 | 1033 | 20.4 | 13.5 | 12.5 | 13.9 | 0.8 |
| GSM5292177 | FALSE | 4070 | 3245 | 825 | 20.3 | 12.5 | 10.3 | 11.1 | 3.4 |
| SRR27882199 | FALSE | 21084 | 16821 | 4263 | 20.2 | 9.5 | 8.6 | 14.9 | 1.2 |
| SRR27882172 | FALSE | 14988 | 12215 | 2773 | 18.5 | 9.4 | 7.9 | 10.8 | 11.7 |
| SRR27882081 | FALSE | 8095 | 6617 | 1478 | 18.3 | 8.1 | 7.7 | 13.0 | 11.0 |
| GSM5292165 | FALSE | 10904 | 9008 | 1896 | 17.4 | 7.1 | 6.7 | 14.6 | 0.6 |
| SRR27882171 | FALSE | 12692 | 10498 | 2194 | 17.3 | 8.0 | 6.6 | 10.6 | 6.6 |
| SRR27882214 | FALSE | 6549 | 5414 | 1135 | 17.3 | 6.7 | 6.7 | 12.9 | 2.8 |
| SRR27882188 | FALSE | 6182 | 5118 | 1064 | 17.2 | 12.1 | 11.2 | 8.2 | 0.6 |
| GSM5292194 | FALSE | 12425 | 10328 | 2097 | 16.9 | 9.0 | 5.7 | 9.0 | 9.0 |
| SRR27882175 | FALSE | 5298 | 4402 | 896 | 16.9 | 10.5 | 9.1 | 10.1 | 7.0 |
| SRR27882073 | FALSE | 5822 | 4842 | 980 | 16.8 | 10.8 | 8.8 | 9.2 | 1.0 |
| GSM5292207 | FALSE | 3668 | 3055 | 613 | 16.7 | 12.4 | 9.8 | 2.6 | 5.6 |
| SRR27882189 | FALSE | 27458 | 22887 | 4571 | 16.6 | 16.3 | 12.2 | 0.8 | 0.2 |
| GSM5292171 | FALSE | 2663 | 2220 | 443 | 16.6 | 9.3 | 8.6 | 10.5 | 2.9 |
| GSM5292197 | FALSE | 9407 | 7912 | 1495 | 15.9 | 7.0 | 5.9 | 11.1 | 5.0 |
| SRR27882169 | FALSE | 11735 | 9922 | 1813 | 15.4 | 7.9 | 6.5 | 7.2 | 9.8 |
| SRR27882077 | FALSE | 14215 | 12041 | 2174 | 15.3 | 4.3 | 3.2 | 10.9 | 13.8 |
| GSM5292199 | FALSE | 8616 | 7299 | 1317 | 15.3 | 5.8 | 4.0 | 9.1 | 12.2 |
| SRR27882205 | FALSE | 7728 | 6587 | 1141 | 14.8 | 7.5 | 7.2 | 9.8 | 1.4 |
| SRR27882082 | FALSE | 11720 | 10025 | 1695 | 14.5 | 7.5 | 5.8 | 7.9 | 10.4 |
| GSM5292176 | FALSE | 7542 | 6447 | 1095 | 14.5 | 11.7 | 9.0 | 3.5 | 1.6 |
| SRR27882216 | FALSE | 8536 | 7303 | 1233 | 14.4 | 5.4 | 5.1 | 11.2 | 1.1 |
| SRR27882163 | FALSE | 11192 | 9593 | 1599 | 14.3 | 8.5 | 7.2 | 9.6 | 3.6 |
| SRR27882150 | FALSE | 8670 | 7438 | 1232 | 14.2 | 9.7 | 7.9 | 1.7 | 5.8 |
| GSM5292203 | FALSE | 5097 | 4376 | 721 | 14.1 | 7.0 | 6.2 | 10.0 | 0.7 |
| SRR27882158 | FALSE | 7103 | 6162 | 941 | 13.2 | 8.7 | 7.5 | 3.5 | 5.9 |
| SRR27882161 | FALSE | 5906 | 5140 | 766 | 13.0 | 8.0 | 7.2 | 7.1 | 3.3 |
| SRR27882094 | FALSE | 10333 | 9005 | 1328 | 12.9 | 8.7 | 7.2 | 1.9 | 5.5 |
| SRR27882181 | FALSE | 13748 | 11984 | 1764 | 12.8 | 3.3 | 3.1 | 10.3 | 10.2 |
| SRR27882159 | FALSE | 6881 | 6001 | 880 | 12.8 | 7.2 | 6.4 | 8.6 | 2.6 |
| SRR27882182 | FALSE | 10809 | 9441 | 1368 | 12.7 | 9.4 | 8.7 | 6.1 | 2.2 |
| SRR27882180 | FALSE | 15818 | 13840 | 1978 | 12.5 | 6.2 | 4.9 | 7.8 | 8.5 |
| SRR27882092 | FALSE | 11841 | 10395 | 1446 | 12.2 | 7.3 | 5.7 | 1.9 | 6.7 |
| SRR27882157 | FALSE | 9256 | 8147 | 1109 | 12.0 | 5.3 | 4.3 | 1.3 | 8.6 |
| GSM5292156 | FALSE | 7433 | 6589 | 844 | 11.4 | 7.6 | 6.2 | 3.7 | 2.9 |
| SRR27882201 | FALSE | 12137 | 10770 | 1367 | 11.3 | 4.8 | 5.1 | 7.8 | 1.7 |
| SRR27882156 | FALSE | 8944 | 7966 | 978 | 10.9 | 7.4 | 6.0 | 1.0 | 5.0 |
| GSM5292175 | FALSE | 7430 | 6634 | 796 | 10.7 | 5.2 | 4.3 | 5.3 | 5.7 |
| SRR27882093 | FALSE | 11990 | 10731 | 1259 | 10.5 | 7.3 | 5.9 | 1.2 | 4.5 |
| GSM5292150 | FALSE | 12051 | 10826 | 1225 | 10.2 | 8.0 | 6.2 | 1.7 | 3.4 |
| SRR27882174 | FALSE | 9724 | 8734 | 990 | 10.2 | 7.3 | 5.6 | 3.7 | 1.9 |
| GSM5292162 | FALSE | 9671 | 8709 | 962 | 9.9 | 3.7 | 2.7 | 5.6 | 7.3 |
| SRR27882177 | FALSE | 10668 | 9643 | 1025 | 9.6 | 4.3 | 4.2 | 6.5 | 6.1 |
| SRR27882086 | FALSE | 8392 | 7604 | 788 | 9.4 | 5.8 | 4.9 | 0.6 | 5.0 |
| GSM5292181 | FALSE | 6573 | 5955 | 618 | 9.4 | 6.6 | 5.3 | 1.0 | 4.6 |
| SRR27882079 | FALSE | 10190 | 9244 | 946 | 9.3 | 4.9 | 4.2 | 5.9 | 6.1 |
| SRR27882075 | FALSE | 14749 | 13388 | 1361 | 9.2 | 5.2 | 4.3 | 4.7 | 5.0 |
| SRR27882091 | FALSE | 12066 | 10962 | 1104 | 9.1 | 4.8 | 3.6 | 0.7 | 5.8 |
| GSM5292178 | FALSE | 6630 | 6036 | 594 | 9.0 | 4.2 | 3.9 | 5.2 | 4.1 |
| SRR27882080 | FALSE | 10818 | 9864 | 954 | 8.8 | 5.7 | 5.0 | 2.5 | 5.2 |
| GSM5292158 | FALSE | 8334 | 7621 | 713 | 8.6 | 6.9 | 5.3 | 2.3 | 2.0 |
| GSM5292152 | FALSE | 5029 | 4599 | 430 | 8.6 | 5.4 | 4.3 | 2.4 | 4.3 |
| SRR27882166 | FALSE | 6434 | 5888 | 546 | 8.5 | 5.4 | 5.2 | 4.4 | 1.3 |
| GSM5292184 | FALSE | 5549 | 5078 | 471 | 8.5 | 5.1 | 4.4 | 4.1 | 1.5 |
| GSM5292160 | FALSE | 12538 | 11482 | 1056 | 8.4 | 5.4 | 4.2 | 2.6 | 3.7 |
| SRR27882154 | FALSE | 10678 | 9792 | 886 | 8.3 | 5.8 | 4.3 | 1.0 | 3.4 |
| SRR27882211 | FALSE | 8684 | 7974 | 710 | 8.2 | 4.4 | 5.3 | 4.1 | 2.1 |
| SRR27882085 | FALSE | 7350 | 6764 | 586 | 8.0 | 5.2 | 4.8 | 1.9 | 3.9 |
| SRR27882191 | FALSE | 5197 | 4782 | 415 | 8.0 | 4.6 | 4.8 | 4.9 | 2.3 |
| SRR27882185 | FALSE | 12895 | 11881 | 1014 | 7.9 | 3.8 | 2.9 | 2.9 | 5.6 |
| SRR27882179 | FALSE | 9922 | 9135 | 787 | 7.9 | 3.9 | 3.0 | 4.2 | 6.1 |
| GSM5292167 | FALSE | 6821 | 6291 | 530 | 7.8 | 6.8 | 5.2 | 1.6 | 0.7 |
| GSM5292168 | FALSE | 3676 | 3391 | 285 | 7.8 | 4.6 | 4.5 | 4.9 | 0.1 |
| GSM5292188 | FALSE | 5879 | 5424 | 455 | 7.7 | 6.2 | 5.2 | 1.5 | 1.6 |
| SRR27882090 | FALSE | 8007 | 7400 | 607 | 7.6 | 5.5 | 5.0 | 0.7 | 2.8 |
| SRR27882153 | FALSE | 8628 | 7981 | 647 | 7.5 | 5.2 | 4.5 | 1.0 | 3.4 |
| GSM5292155 | FALSE | 6601 | 6114 | 487 | 7.4 | 4.1 | 2.8 | 1.5 | 5.2 |
| GSM5292146 | FALSE | 10398 | 9646 | 752 | 7.2 | 3.7 | 2.6 | 2.2 | 5.0 |
| SRR27882207 | FALSE | 7070 | 6561 | 509 | 7.2 | 4.9 | 4.3 | 1.3 | 3.3 |
| GSM5292191 | FALSE | 8859 | 8233 | 626 | 7.1 | 2.6 | 2.2 | 1.0 | 5.9 |
| GSM5292187 | FALSE | 7203 | 6690 | 513 | 7.1 | 5.6 | 4.9 | 1.5 | 1.5 |
| SRR27882198 | FALSE | 4879 | 4533 | 346 | 7.1 | 3.1 | 2.8 | 4.2 | 5.0 |
| SRR27882209 | FALSE | 8418 | 7826 | 592 | 7.0 | 3.8 | 3.6 | 2.7 | 4.0 |
| GSM5292148 | FALSE | 11077 | 10320 | 757 | 6.8 | 3.9 | 3.5 | 2.6 | 4.1 |
| SRR27882167 | FALSE | 9423 | 8783 | 640 | 6.8 | 4.6 | 3.8 | 3.2 | 2.0 |
| SRR27882149 | FALSE | 9245 | 8612 | 633 | 6.8 | 4.2 | 3.4 | 0.3 | 3.5 |
| GSM5292186 | FALSE | 8565 | 7984 | 581 | 6.8 | 4.0 | 2.9 | 2.4 | 3.5 |
| GSM5292151 | FALSE | 10250 | 9564 | 686 | 6.7 | 5.1 | 3.2 | 0.7 | 2.5 |
| GSM5292149 | FALSE | 14344 | 13397 | 947 | 6.6 | 3.8 | 2.8 | 2.4 | 4.1 |
| GSM5292180 | FALSE | 7656 | 7150 | 506 | 6.6 | 3.0 | 2.6 | 4.4 | 2.9 |
| SRR27882196 | FALSE | 4869 | 4556 | 313 | 6.4 | 3.8 | 3.2 | 1.9 | 3.5 |
| SRR27882178 | FALSE | 12062 | 11304 | 758 | 6.3 | 4.2 | 3.4 | 2.2 | 3.1 |
| GSM5292170 | FALSE | 4021 | 3766 | 255 | 6.3 | 4.7 | 4.4 | 1.4 | 1.5 |
| SRR27882164 | FALSE | 14729 | 13826 | 903 | 6.1 | 3.9 | 2.9 | 2.5 | 1.9 |
| GSM5292143 | FALSE | 10348 | 9732 | 616 | 6.0 | 4.2 | 3.4 | 1.6 | 2.7 |
| SRR27882187 | FALSE | 9207 | 8650 | 557 | 6.0 | 3.9 | 3.2 | 2.7 | 1.5 |
| SRR27882212 | FALSE | 8641 | 8122 | 519 | 6.0 | 4.7 | 4.1 | 1.0 | 2.0 |
| GSM5292147 | FALSE | 12168 | 11447 | 721 | 5.9 | 3.6 | 2.5 | 1.8 | 3.8 |
| GSM5292157 | FALSE | 8897 | 8385 | 512 | 5.8 | 3.0 | 2.1 | 0.9 | 3.6 |
| SRR27882208 | FALSE | 8891 | 8382 | 509 | 5.7 | 3.7 | 3.8 | 2.6 | 1.3 |
| SRR27882074 | FALSE | 8758 | 8261 | 497 | 5.7 | 4.4 | 3.7 | 1.7 | 1.6 |
| GSM5292163 | FALSE | 13090 | 12359 | 731 | 5.6 | 3.7 | 2.4 | 1.1 | 2.6 |
| SRR27882194 | FALSE | 4994 | 4720 | 274 | 5.5 | 2.7 | 2.2 | 2.8 | 3.8 |
| GSM5292201 | FALSE | 6508 | 6155 | 353 | 5.4 | 2.9 | 2.4 | 2.9 | 3.2 |
| GSM5292183 | FALSE | 1720 | 1627 | 93 | 5.4 | 3.0 | 3.2 | 0.2 | 2.2 |
| GSM5292153 | FALSE | 7785 | 7373 | 412 | 5.3 | 4.5 | 3.5 | 0.9 | 1.2 |
| GSM5292144 | FALSE | 13721 | 13012 | 709 | 5.2 | 3.7 | 3.1 | 1.3 | 2.0 |
| SRR27882088 | FALSE | 8509 | 8067 | 442 | 5.2 | 2.2 | 1.8 | 0.2 | 3.6 |
| SRR27882204 | FALSE | 13518 | 12846 | 672 | 5.0 | 3.6 | 2.7 | 0.8 | 2.0 |
| GSM5292174 | FALSE | 7198 | 6838 | 360 | 5.0 | 3.8 | 3.1 | 1.1 | 1.5 |
| SRR27882152 | FALSE | 8563 | 8149 | 414 | 4.8 | 3.6 | 2.9 | 0.5 | 1.5 |
| GSM5292205 | FALSE | 8031 | 7654 | 377 | 4.7 | 2.4 | 1.9 | 0.9 | 3.2 |
| SRR27882084 | FALSE | 7167 | 6829 | 338 | 4.7 | 2.5 | 2.3 | 1.1 | 3.2 |
| SRR27882173 | FALSE | 9927 | 9493 | 434 | 4.4 | 2.8 | 2.6 | 1.7 | 2.2 |
| SRR27882151 | FALSE | 9167 | 8772 | 395 | 4.3 | 2.8 | 2.2 | 0.4 | 2.0 |
| GSM5292172 | FALSE | 5249 | 5023 | 226 | 4.3 | 1.9 | 1.7 | 2.1 | 1.3 |
| GSM5292166 | FALSE | 9080 | 8695 | 385 | 4.2 | 3.1 | 2.1 | 0.9 | 1.7 |
| SRR27882213 | FALSE | 8590 | 8244 | 346 | 4.0 | 1.8 | 1.6 | 1.8 | 2.7 |
| SRR27882210 | FALSE | 5861 | 5640 | 221 | 3.8 | 1.6 | 1.6 | 1.6 | 2.6 |
| GSM5292145 | FALSE | 6349 | 6116 | 233 | 3.7 | 2.9 | 3.4 | 0.4 | 0.0 |
| SRR27882089 | FALSE | 8051 | 7762 | 289 | 3.6 | 2.0 | 1.4 | 0.2 | 2.0 |
| SRR27882186 | FALSE | 9149 | 8826 | 323 | 3.5 | 2.2 | 1.8 | 1.5 | 1.4 |
| SRR27882202 | FALSE | 7345 | 7090 | 255 | 3.5 | 1.8 | 1.7 | 1.6 | 1.2 |
| SRR27882148 | FALSE | 7712 | 7452 | 260 | 3.4 | 2.0 | 1.9 | 0.7 | 1.6 |
| SRR27882215 | FALSE | 6847 | 6617 | 230 | 3.4 | 1.9 | 1.7 | 1.2 | 1.8 |
| GSM5292202 | FALSE | 7689 | 7465 | 224 | 2.9 | 2.0 | 1.7 | 0.6 | 1.0 |
| SRR27882193 | FALSE | 6295 | 6120 | 175 | 2.8 | 1.6 | 1.4 | 1.1 | 1.1 |
| GSM5292154 | FALSE | 6756 | 6572 | 184 | 2.7 | 2.1 | 1.7 | 0.2 | 0.6 |
| SRR27882078 | FALSE | 10122 | 9856 | 266 | 2.6 | 2.1 | 1.7 | 0.6 | 0.9 |
| GSM5292164 | FALSE | 11633 | 11341 | 292 | 2.5 | 1.4 | 1.0 | 0.1 | 1.4 |
| GSM5292208 | FALSE | 8830 | 8687 | 143 | 1.6 | 1.0 | 0.7 | 0.1 | 0.8 |
What were the reasons for excluding barcodes?
An upset plot is generated for each sample to visualize the reasons for barcode exclusion. The plot shows the overlap between different exclusion criteria, with vertical bars representing the size of each intersection. Plots are omitted for samples where no barcodes were excluded.
for (bb in b_lvls) {
qc_tmp = qc_dt[ batch_var == bb ]
if (nrow(qc_tmp) == 1 | sum(qc_tmp$keep) == nrow(qc_tmp))
next
cat('### ', bb, '\n')
suppressMessages( print(plot_upset_of_exclusions(qc_tmp, qc_names, qc_lu, cuts_dt)) )
cat('\n\n')
}GSM5292146
GSM5292147
GSM5292156
GSM5292157
GSM5292158
GSM5292200
SRR27882183
SRR27882182
SRR27882181
SRR27882171
SRR27882170
SRR27882169
SRR27882094
SRR27882093
SRR27882092
SRR27882091
SRR27882090
SRR27882089
SRR27882088
SRR27882086
SRR27882085
SRR27882084
SRR27882158
SRR27882157
SRR27882156
SRR27882154
SRR27882153
SRR27882152
SRR27882151
SRR27882150
SRR27882149
SRR27882148
GSM5292143
GSM5292144
GSM5292145
GSM5292148
GSM5292149
GSM5292150
GSM5292151
GSM5292152
GSM5292153
GSM5292154
GSM5292155
GSM5292194
GSM5292195
GSM5292196
GSM5292197
GSM5292198
GSM5292199
SRR27882082
SRR27882081
SRR27882080
SRR27882079
SRR27882078
SRR27882077
SRR27882075
SRR27882074
SRR27882073
SRR27882180
SRR27882179
SRR27882178
SRR27882177
SRR27882175
SRR27882174
SRR27882173
SRR27882172
GSM5292174
GSM5292175
GSM5292176
GSM5292177
GSM5292178
GSM5292179
GSM5292180
GSM5292181
GSM5292182
GSM5292183
GSM5292184
GSM5292185
GSM5292186
GSM5292187
GSM5292188
GSM5292193
GSM5292201
SRR27882193
SRR27882192
SRR27882191
SRR27882190
SRR27882189
SRR27882188
SRR27882187
SRR27882186
SRR27882185
SRR27882165
SRR27882164
SRR27882163
SRR27882162
SRR27882161
SRR27882160
SRR27882159
GSM5292164
GSM5292169
GSM5292173
GSM5292190
GSM5292191
GSM5292192
GSM5292202
GSM5292203
GSM5292204
GSM5292205
GSM5292206
GSM5292207
GSM5292208
SRR27882214
SRR27882212
SRR27882203
SRR27882202
SRR27882201
SRR27882200
SRR27882199
SRR27882198
SRR27882197
SRR27882196
SRR27882194
GSM5292159
GSM5292160
GSM5292161
GSM5292162
GSM5292163
GSM5292165
GSM5292166
GSM5292167
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GSM5292170
GSM5292171
GSM5292172
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SRR27882168
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SRR27882166
SRR27882216
SRR27882215
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SRR27882210
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R session info
Details of the R package versions used are given below.
devtools::session_info()## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.4.3 (2025-02-28)
## os Red Hat Enterprise Linux 8.10 (Ootpa)
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Europe/Zurich
## date 2026-03-04
## pandoc 3.8.2.1 @ /home/macnairw/packages/scprocess/.snakemake/conda/4fef11cadd34f9d2d13a0d6139d09340_/bin/ (via rmarkdown)
## quarto NA
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
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## assertthat * 0.2.1 2019-03-21 [1] CRAN (R 4.4.3)
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## BiocIO 1.16.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2)
## BiocManager 1.30.27 2025-11-14 [1] CRAN (R 4.4.3)
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## GlobalOptions 0.1.2 2020-06-10 [1] CRAN (R 4.4.3)
## glue 1.8.0 2024-09-30 [1] CRAN (R 4.4.3)
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## htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.3)
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##
## ──────────────────────────────────────────────────────────────────────────────