hts-tools 0.0.3

Parsing and analysing platereader absorbance and fluorescence data.

🏮 hts-tools

Parsing and analysing platereader absorbance and fluorescence data.

• Installation
• Command-line usage
  • First pipeline example
    • Parsing platereader exports
    • Adding experimental conditions
    • Normalization within batches
    • Plotting dose responses
  • Second pipeline example
    • Converting plate-shaped data to columns
    • Statistical testing
  • Other commands
• Python API
• Documentation

Installation

The easy way

Install the pre-compiled version from PyPI:

pip install hts-tools

From source

Clone the repository, then cd into it. Then run:

pip install -e .

Command-line usage

hts-tools provides command-line utlities to analyse and plot data from platereaders, starting with the raw exported data with no manual conversion or copy-pasting needed. The tools complete specific tasks which can be easily composed into analysis pipelines, because the TSV table output goes to stdout by default so they can be piped from one tool to another.

To get a list of commands (tools), do

hts --help

And to get help for a specific command, do

hts <command> --help

For the Python API, see below.

First pipeline example

This command takes several exported Excel files (matching the pattern plate-?.xlsx) from a Biotek platereader, adds annotations on experimental conditions, and normalizes the data based on positive and negative controls. Finally, dose-response curves are plotted.

hts parse plate-?.xlsx --data-shape row --vendor Biotek \
    | hts join --right layout.xlsx \
    | hts normalize --control compound_name \
        --positive RIF --negative DMSO \
        --grouping plate_id --method npg \
    | hts plot-dose -x concentration --facets guide_name --color compound_name \
        --output plt-test

Parsing platereader exports

The command hts parse converts Excel or CSV or TSV files exported from platereader software from a specified vendor into a uniform columnar table format used by all downstream hts-tools. The data-shape option indicates whether the export was in plate format or row-wise table format. It should usually be the first command in a pipeline.

hts parse produces a table with at least the following columns (with example entries):

row_id	column_id	well_id	plate_id	data_filename	data_sheet	measured_abs_ch1	abs_ch1_wavelength
A	1	A01	Plate 6	plate-6.xlsx	Plate6 - Sheet 1	0.366	600nm
A	2	A02	Plate 6	plate-6.xlsx	Plate6 - Sheet 1	0.402	600nm

If only fluorescence was measured, the last two columns would be called measured_fluor_ch1 and fluor_ch1_wavelength. If there were multiple measurements, then they will appear as additional columns with increasing ch (channel) numbers, for example, measured_fluor_ch2, fluor_ch2_wavelength.

There will also be additional columns using information scraped from the input file. These will usually have headings starting with meta_, such as meta_protocol_file_path, meta_date, meta_time, and meta_reader_serial_number.

Adding experimental conditions

The output from hts parse is passed to hts join, which combines two tables based on values in shared columns (known as a database join). For example, if layout.xlsx contains a sheet with this table:

column_id	plate_id	compound_name
2	Plate 6	trimethoprim
1	Plate 6	moxifloxacin

then hts parse plate-?.xlsx --data-shape row | hts join --right layout.xlsx will result in

row_id	column_id	well_id	plate_id	data_filename	data_sheet	measured_abs_ch1	abs_ch1_wavelength	compound_name
A	1	A01	Plate 6	plate-6.xlsx	Plate6 - Sheet 1	0.366	600nm	moxifloxacin
A	2	A02	Plate 6	plate-6.xlsx	Plate6 - Sheet 1	0.402	600nm	trimethoprim

Since column_id and plate_id are the only column headings in common, the entries of these columns are used to match the rows of the tables. So where column_id = 2, compound_name = trimethoprim will be added.

If you join an Excel XLSX file containing multiple sheets, these will each be joined in order. In this way, you can add experimental conditions easily by, for example, first joining the conditions that vary by plate and row (such as compound), then by column (such as concentration). This approach is very flexible, and you can join on any number of columns and add any new ones you like as long as the column headings aren't repeated.

Normalization within batches

The hts normalize command normalizes raw measured data based on controls. This can add power to downstream statsical analyses by mitigating batch-to-batch variation.

hts normalize adds new columns for each measured column. These columns start with calc_ and end with _norm.{method}, for example calc_abs_ch1_norm.npg and calc_abs_ch2_norm.npg. Two methods are offered which optionally normalize within within groups, such as batches or plates.

Normalized proportion of growth (NPG)

This method scales raw data to be between $0$ and $1$ based on positive and negative controls, optionally within groups (or batches) of measurements. In the example above, the positive and negative controls are defined as RIF and DMSO, and should be found in the column compound_name (which may have been added by hts join).

The positive and negative controls are averaged within each value in the --grouping column. In the example above, they will be averaged for each plate_id, and these will be used to normalize the measured values of that plate_id according to:

$$s = \frac{m - \mu_p}{\mu_n - \mu_p}$$

where $s$ is the normalized value, $m$ is the measured value, and $\mu_p$ and $\mu_n$ are the mean positive and negative controls.

Proportion of negative (PON) [default]

This method scales raw data relative negative controls only, optionally within groups (or batches) of measurements.

The negative controls are averaged within each value in the --grouping column. In the example above, they would be averaged for each plate_id, and these will be used to normalize the measured values of that plate_id according to:

$$s = \frac{m}{\mu_n}$$

where $s$ is the normalized value, $m$ is the measured value, and $\mu_n$ is the mean negative control.

Plotting dose response

hts plot-dose is a very flexible command which takes the columnar tables as input and plots the data in almost any breakdown using a color-blind palette. The required -x option indicates which column to use as the x-axis (usually concentration). The y-axis will be values in all the measured and calculated columns (hts plot-dr plots them all automatically in seaparte files). The other options allow splitting the plots by file, facet (panel) and color according to the values in columns.

The example above, hts plot-dose -x concentration --facets guide_name --color compound_name, will produce plots like this:

The panels each value with the same guide_name is in a facet (panel), and the lines are colored by compound_name.

Second pipeline example

Here is another example showing the sequential use of hts join to join two tables of experimental data, and two other commands: hts pivot and hts summarize.

hts pivot compounds.xlsx \
      --name compound_name

hts parse plate-*.txt --data-shape plate \
    | hts join --right sample-sheet.csv \
    | hts join --right pivoted-compounds.tsv \
    | hts normalize --control compound_name --positive RIF --negative DMSO --grouping strain_name plate_id \
    | hts summarize --control compound_name --positive RIF --negative DMSO --grouping strain_name compound_name --plot summary \
    > summary.tsv

These commands are explained below.

Converting plate shaped data to columns

Sometimes you will want to use data, such as plate layouts, which are in a plate-shaped layout instead of a column format. For example:

You can convert this to column format using hts pivot, which produces a table in the following format:

row_id	column_id	compound_name	well_id	plate_id	filename
C	2	RIF	C02	Plate 7	compounds.xlsx
D	2	LYSINE	D02	Plate 7	compounds.xlsx
E	2	DMSO	E02	Plate 7	compounds.xlsx
F	2	RIF	F02	Plate 7	compounds.xlsx

It is assumed that there is one plate per sheet for Excel files, and one plate per file for TSV and CSV files. The plate name is taken from the sheet name (Excel) or filename (other formats).

You can prepend the names of the plate_id and filename columns with the -x option. for example, hts pivot compounds.xlsx -x compound_source --name compound_name would have columns compound_source_plate_id compound_source_filename. This is helpful when usign hts join later where the plate and filename columns would otherwise be shared but have different meanings and values, and you don't want to accidentally join on them.

Statistical testing

Groups of values (such as replicates) can be compared against a negative control for statistical testing using hts summarize. The --grouping option indicates the columns whose values together indicate values which are replicates of a particular condition of interest. For example, --grouping strain_name compound_name would indicate that values which have the same strain_name and compound_name are replicates.

Statistical tests compare to the --negative values, and use all measured and normalized (calc_*_norm) columns. Currently, the Student's t-test and Mann-whitney U-test are implemented. The t-test is best suited to Normal-distributed data while the MWU is better for other distributions which might not have a nice bell curve distribution.

Although hts summarize calcualtes both tests simultaneously, it's not a good idea to look for "significant" $p$-values in both. This is called p-hacking, and leads to false positives. Instead, decide which test is most appropriate for your data and stick with that one.

This command also calculates other summary statistics such as between-replicate mean, variance, and SSMD. If a filename prefix is provided to the --plot option, then volcano and flashlight plots are produced, which may be useful for identifying hits of high throughput screens.

Other commands

There are several other commands from hts-tools which take as input the output from hts parse, joined to an experimental data table (layout.xlsx in these examples).

• hts qc

Do quality control checks by calculating mean, standard deviation, Z'-factor, and SSMD, and plotting them.

hts parse plate-?.xlsx --data-shape row  \
  | hts join --right layout.xlsx \
  | hts qc --control compound_name --positive RIF --negative DMSO --grouping strain_name plate_id --plot qc-plot \
  > qc.tsv

• hts plot-hm

Plot heatmaps of signal intensity arranged by plate well. This can be useful to identify unwanted within-plate variability.

hts parse plate-?.xlsx --data-shape row \
  | hts join --right layout.xlsx \
  | hts plot-hm --grouping strain_name sample_id plate_id --output hm

Here, --grouping identifies the columns which indicate values coming from the same plate. One file is produced per measured and normalized (calc_*_norm) column.

• hts plot-rep

Plot two replicates against each other for each condition.

hts parse plate-?.xlsx --data-shape row  \
  | hts join --right layout.xlsx \
  | hts plot-rep --control compound_name --positive RIF --negative DMSO --grouping strain_name compound_name --output rep

Here, --grouping identifies the unique conditions within which values are treated as replicates. The positives and negatives are plotted as different colors. One file is produced per measured and normalized (calc_*_norm) column.

In the plots, the left column is on a linear-linear scale and the right column is on a log-log scale. There is one row of plots per wavelength set in the dataset.

• hts plot-hist

Plot histograms of the data values.

hts parse plate-?.xlsx --data-shape row \
  | hts join --right layout.xlsx \
  | hts plot-hist --control compound_name --positive RIF --negative DMSO --output hist

The positives and negatives are plotted as different colors. One file is produced per measured and normalized (calc_*_norm) column.

In the plots, the left two columns are on a linear-linear scale and the right two columns are on a log-log scale. There is one row of plots per wavelength set in the dataset.

Python API

hts-tools can be imported into Python to help make custom analyses.

>>> import htstools as hts

You can read raw exports from platereader software into a columnar Pandas dataframe.

>>> hts.from_platereader("plates.xlsx", shape="plate", vendor="Biotek")

Once in the columnar format, you can annotate experimental conditions.

>>> import pandas as pd
>>> a = pd.DataFrame(dict(column=['A', 'B', 'A', 'B'], 
...                       abs=[.1, .2, .23, .11]))
>>> a  
    column   abs
0      A  0.10
1      B  0.20
2      A  0.23
3      B  0.11
>>> b = pd.DataFrame(dict(column=['B', 'A'], 
...                       drug=['TMP', 'RIF']))
>>> b  
    column drug
0      B  TMP
1      A  RIF
>>> shared_cols, data = join(a, b)
>>> shared_cols
('column',)
>>> data 
column   abs drug
0      A  0.10  RIF
1      A  0.23  RIF
2      B  0.20  TMP
3      B  0.11  TMP

If the conditions to annotate are in a plate-shaped format, you can melt them into a columnar format before joining.

>>> import pandas as pd
>>> import numpy as np
>>> a = pd.DataFrame(index=list("ABCDEFGH"), 
...                  columns=range(1, 13), 
...                  data=np.arange(1, 97).reshape(8, 12))
>>> a  
    1   2   3   4   5   6   7   8   9   10  11  12
A   1   2   3   4   5   6   7   8   9  10  11  12
B  13  14  15  16  17  18  19  20  21  22  23  24
C  25  26  27  28  29  30  31  32  33  34  35  36
D  37  38  39  40  41  42  43  44  45  46  47  48
E  49  50  51  52  53  54  55  56  57  58  59  60
F  61  62  63  64  65  66  67  68  69  70  71  72
G  73  74  75  76  77  78  79  80  81  82  83  84
H  85  86  87  88  89  90  91  92  93  94  95  96
>>> hts.pivot_plate(a, value_name="well_number")  
    row_id column_id  well_number well_id plate_id
0       A         1            1     A01         
1       B         1           13     B01         
2       C         1           25     C01         
3       D         1           37     D01         
4       E         1           49     E01         
..    ...       ...          ...     ...      ...
91      D        12           48     D12         
92      E        12           60     E12         
93      F        12           72     F12         
94      G        12           84     G12         
95      H        12           96     H12         

[96 rows x 5 columns]

This also works on the multi-sheet dictionary output of pd.read_excel(..., sheet_names=None).

>>> hts.pivot_plate({'sheet_1': a}, value_name="well_number")    
row_id column_id  well_number well_id plate_id
0       A         1            1     A01  sheet_1
1       B         1           13     B01  sheet_1
2       C         1           25     C01  sheet_1
3       D         1           37     D01  sheet_1
4       E         1           49     E01  sheet_1
..    ...       ...          ...     ...      ...
91      D        12           48     D12  sheet_1
92      E        12           60     E12  sheet_1
93      F        12           72     F12  sheet_1
94      G        12           84     G12  sheet_1
95      H        12           96     H12  sheet_1

[96 rows x 5 columns]

Replicates within condition groups can be annotated.

>>> import pandas as pd
>>> a = pd.DataFrame(dict(group=['g1', 'g1', 'g2', 'g2'], 
...                       control=['n', 'n', 'p', 'p'], 
...                       m_abs_ch1=[.1, .2, .9, .8], 
...                       abs_ch1_wavelength=['600nm'] * 4))
>>> a 
    group control  m_abs_ch1 abs_ch1_wavelength
0    g1       n        0.1              600nm
1    g1       n        0.2              600nm
2    g2       p        0.9              600nm
3    g2       p        0.8              600nm
>>> hts.replicate_table(a, group='group') 
    group control  m_abs_ch1 abs_ch1_wavelength  replicate
0    g1       n        0.1              600nm          1
1    g1       n        0.2              600nm          2
2    g2       p        0.9              600nm          2
3    g2       p        0.8              600nm          1

If you prefer, you can get a "wide" output.

>>> hts.replicate_table(a, group='group', wide='m_abs_ch1') 
replicate  rep_1  rep_2
group                  
g1           0.2    0.1
g2           0.8    0.9

Values can be normalized to values between 0 and 1 relative to their positive (0%) and negative (100%) controls, optinally within groups or batches.

>>> import pandas as pd
>>> a = pd.DataFrame(dict(control=['n', 'n', '', '', 'p', 'p'], 
...                  m_abs_ch1=[.1, .2, .5, .4, .9, .8], 
...                  abs_ch1_wavelength=['600nm'] * 6))
>>> a 
    control  m_abs_ch1 abs_ch1_wavelength
0       n        0.1              600nm
1       n        0.2              600nm
2                0.5              600nm
3                0.4              600nm
4       p        0.9              600nm
5       p        0.8              600nm
>>> hts.normalize(a, control_col='control', pos='p', neg='n', measurement_col='m_abs_ch1') 
    control  m_abs_ch1 abs_ch1_wavelength  m_abs_ch1_neg_mean  m_abs_ch1_pos_mean  m_abs_ch1_norm
0       n        0.1              600nm                0.15                0.85        1.071429
1       n        0.2              600nm                0.15                0.85        0.928571
2                0.5              600nm                0.15                0.85        0.500000
3                0.4              600nm                0.15                0.85        0.642857
4       p        0.9              600nm                0.15                0.85       -0.071429
5       p        0.8              600nm                0.15                0.85        0.071429

The scaling can be reversed with flip=True.

>>> hts.normalize(a, control_col='control', pos='p', neg='n', measurement_col='m_abs_ch1', flip=True) 
    control  m_abs_ch1 abs_ch1_wavelength  m_abs_ch1_neg_mean  m_abs_ch1_pos_mean  m_abs_ch1_norm
0       n        0.1              600nm                0.15                0.85       -0.071429
1       n        0.2              600nm                0.15                0.85        0.071429
2                0.5              600nm                0.15                0.85        0.500000
3                0.4              600nm                0.15                0.85        0.357143
4       p        0.9              600nm                0.15                0.85        1.071429
5       p        0.8              600nm                0.15                0.85        0.928571

Summary statstics and statsitcial tests relative to the negative controls can be generated.

>>> a = pd.DataFrame(dict(gene=['g1', 'g1', 'g2', 'g2', 'g1', 'g1', 'g2', 'g2'], 
    ...                       compound=['n', 'n', 'n', 'n', 'cmpd1', 'cmpd1', 'cmpd2', 'cmpd2'], 
    ...                       m_abs_ch1=[.1, .2, .9, .8, .1, .3, .5, .45], 
    ...                       abs_ch1_wavelength=['600nm'] * 8))
    >>> a 
        gene compound  m_abs_ch1 abs_ch1_wavelength
    0    g1        n       0.10              600nm
    1    g1        n       0.20              600nm
    2    g2        n       0.90              600nm
    3    g2        n       0.80              600nm
    4    g1    cmpd1       0.10              600nm
    5    g1    cmpd1       0.30              600nm
    6    g2    cmpd2       0.50              600nm
    7    g2    cmpd2       0.45              600nm
    >>> hts.summarize(a, measurement_col='m_abs_ch1', control_col='compound', neg='n', group='gene')  
      gene abs_ch1_wavelength  m_abs_ch1_mean  m_abs_ch1_std  ...  m_abs_ch1_t.stat  m_abs_ch1_t.p  m_abs_ch1_ssmd  m_abs_ch1_log10fc
    0   g1              600nm          0.1750       0.095743  ...          0.361158       0.742922        0.210042           0.066947
    1   g2              600nm          0.6625       0.221265  ...         -1.544396       0.199787       -0.807183          -0.108233

    [2 rows x 12 columns]
    >>> hts.summarize(a, measurement_col='m_abs_ch1', control_col='compound', neg='n', group=['gene', 'compound'])
    gene compound abs_ch1_wavelength  m_abs_ch1_mean  ...  m_abs_ch1_t.stat  m_abs_ch1_t.p  m_abs_ch1_ssmd  m_abs_ch1_log10fc
    0   g1        n              600nm           0.150  ...          0.000000       1.000000        0.000000           0.000000
    1   g2        n              600nm           0.850  ...          0.000000       1.000000        0.000000           0.000000
    2   g1    cmpd1              600nm           0.200  ...          0.447214       0.711723        0.316228           0.124939
    3   g2    cmpd2              600nm           0.475  ...         -6.708204       0.044534       -4.743416          -0.252725

    [4 rows x 13 columns]

Documentation

Full API documentation is at ReadTheDocs.