import pandas as pd
%load_ext rpy2.ipython
%%R
library(ggplot2)
library(RColorBrewer)
library(ggpubr)
Gel run on 3/26/22
Read gel quantification.
df = pd.read_csv('2022-03-26_15h31m30s-T7Init-midi-preps-1ul-sanity-check.csv')
Remove pFC53 and pFC9 lanes
df = df.loc[~df['Band_Label'].isin(('pFC53', 'pFC9'))]
df = df.sort_values('insert_num')
Plot concentrations measured relative to pFC53 and pFC9 supercoiled bands.
%%R -i df -w 7 -h 5 --units in -r 200
barplot <- ggplot(df, aes(x=as.factor(insert_num), y=Abs.Quant.)) +
geom_bar(
stat='identity', color='black', fill='dodgerblue', position='dodge',
width=0.70
) + theme_pubr() + coord_flip() +
labs(y='Concentration (ng/ul)',
x='Insert',
title='T7Init Series midi preps concentration measurement by agarose gel') +
theme(text = element_text(size = 8))
boxplot <- ggplot(df, aes(y=Abs.Quant.)) + geom_boxplot(fill='tan') + theme_pubr() +
labs(y='Concentration (ng/ul)') +
theme(axis.title.x=element_blank(),
axis.text.x=element_blank(),
axis.ticks.x=element_blank()
)
quant.plot <- ggarrange(barplot, boxplot, widths=c(1, 0.7))
quant.plot
%%R
ggsave(
"2022-03-26_15h31m30s-T7Init-midi-preps-1ul-sanity-check.csv.quant.plot.png",
quant.plot,
dpi=300
)
R[write to console]: Saving 6.67 x 6.67 in image
Make spreadsheet describing volumes to add of each construct to create T7InitVRMix-1.
CON_PER_INSERT = 10 # ng / ul
TOTAL_VOLUME = 300 # ul
df['ul_add_to_mix'] = CON_PER_INSERT * TOTAL_VOLUME / df['Abs.Quant.']
mix = df[["Band_Label", 'ul_add_to_mix', "insert_num", "Abs.Quant."]]
mix = mix.sort_values('insert_num')
print(mix.to_markdown(index=False))
| Band_Label | ul_add_to_mix | insert_num | Abs.Quant. | |:-------------|----------------:|-------------:|-------------:| | VR1 | 3.15808 | 1 | 949.945 | | VR2 | 3.37399 | 2 | 889.155 | | VR3 | 4.68847 | 3 | 639.868 | | VR4 | 7.74572 | 4 | 387.311 | | VR5 | 4.35732 | 5 | 688.496 | | VR6 | 5.69779 | 6 | 526.52 | | VR7 | 2.84563 | 7 | 1054.25 | | VR8 | 7.85345 | 8 | 381.998 | | VR9 | 4.82521 | 9 | 621.734 | | VR10 | 2.9479 | 10 | 1017.67 | | VR11 | 3.71493 | 11 | 807.552 | | VR12 | 5.94932 | 12 | 504.259 | | VR13 | 5.44227 | 13 | 551.24 | | VR14 | 2.75593 | 14 | 1088.56 | | VR15 | 3.74733 | 15 | 800.571 | | VR16 | 3.78123 | 16 | 793.392 | | VR17 | 2.89164 | 17 | 1037.47 | | VR18 | 3.02504 | 18 | 991.723 | | VR19 | 2.89629 | 19 | 1035.81 | | VR20 | 2.08432 | 20 | 1439.32 | | VR21 | 2.35206 | 21 | 1275.48 | | VR22 | 4.25264 | 22 | 705.444 | | VR23 | 2.77091 | 23 | 1082.68 | | VR24 | 2.86016 | 24 | 1048.89 | | VR25 | 2.61526 | 25 | 1147.11 | | VR26 | 4.16159 | 26 | 720.878 | | VR27 | 2.47214 | 27 | 1213.52 | | VR28 | 4.02208 | 28 | 745.883 | | VR29 | 2.5868 | 29 | 1159.74 | | VR30 | 2.61421 | 30 | 1147.57 | | VR31 | 4.54334 | 31 | 660.307 |
print('Volume TE:', round(TOTAL_VOLUME-sum(mix['ul_add_to_mix']), 3))
Volume TE: 180.967
mix.to_csv('T7InitMix-1-construct-volumes.csv')
qu = pd.read_csv('QuBit-T7Measures3-3_26_28.csv')
qu.head()
| Insert | Dilution total volume | Measure 1 | Measure 2 | Measure 3 | Stock concentration | Fold Difference 3/4 measurements | |
|---|---|---|---|---|---|---|---|
| 0 | 1 | 400 | 0.534 | 0.520 | 0.513 | 208.933333 | -0.642849 |
| 1 | 2 | 400 | 0.622 | 0.606 | 0.603 | 244.133333 | -0.440061 |
| 2 | 3 | 400 | 0.434 | 0.426 | 0.420 | 170.666667 | -0.622419 |
| 3 | 4 | 400 | 0.283 | 0.268 | 0.268 | 109.200000 | -0.368786 |
| 4 | 5 | 400 | 3.600 | 3.560 | 3.540 | 1426.666667 | 3.919540 |
merge = pd.merge(mix, qu, left_on='insert_num', right_on='Insert')
merge.head()
| Band_Label | ul_add_to_mix | insert_num | Abs.Quant. | Insert | Dilution total volume | Measure 1 | Measure 2 | Measure 3 | Stock concentration | Fold Difference 3/4 measurements | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | VR1 | 3.158078 | 1.0 | 949.944817 | 1 | 400 | 0.534 | 0.520 | 0.513 | 208.933333 | -0.642849 |
| 1 | VR2 | 3.373992 | 2.0 | 889.154508 | 2 | 400 | 0.622 | 0.606 | 0.603 | 244.133333 | -0.440061 |
| 2 | VR3 | 4.688466 | 3.0 | 639.868137 | 3 | 400 | 0.434 | 0.426 | 0.420 | 170.666667 | -0.622419 |
| 3 | VR4 | 7.745721 | 4.0 | 387.310637 | 4 | 400 | 0.283 | 0.268 | 0.268 | 109.200000 | -0.368786 |
| 4 | VR5 | 4.357324 | 5.0 | 688.495993 | 5 | 400 | 3.600 | 3.560 | 3.540 | 1426.666667 | 3.919540 |
merge['fold_change_gel_qubut'] = merge['Abs.Quant.'] / merge['Stock concentration'] - 1
%%R -i merge -w 7 -h 5 --units in -r 200
barplot.qu <- ggplot(merge, aes(x=as.factor(insert_num), y=fold_change_gel_qubut)) +
geom_bar(
stat='identity', color='black', fill='pink', position='dodge',
width=0.70
) + theme_pubr() + coord_flip() +
labs(y='Fold change',
x='Insert',
title='Fold change ') +
theme(text = element_text(size = 8))
boxplot.qu <- ggplot(merge, aes(y=fold_change_gel_qubut)) + geom_boxplot(fill='lavender') + theme_pubr() +
labs(y='Fold change agarose gel vs. QuBit quantification') +
theme(axis.title.x=element_blank(),
axis.text.x=element_blank(),
axis.ticks.x=element_blank()
)
quant.plot.qu <- ggarrange(barplot.qu, boxplot.qu, widths=c(1, 0.7))
quant.plot.qu
%%R
ggsave(
"2022-03-26_15h31m30s-T7Init-midi-preps-1ul-sanity-check.csv.quant.quBit.fold.change.plot.png",
quant.plot.qu,
dpi=300
)
R[write to console]: Saving 6.67 x 6.67 in image