Table Compute

Example 1: Sub-selecting from a table

We have the following table:

.	c1	c2	c3
g1	10	20	30
g2	3	6	9
g3	4	8	12
g4	81	6	3

and we want to duplicate c1 and remove c2. Also select g1 to g3 and add g2 at the end as well. This

would result in the output table:

.	c1	c1	c3
g1	10	10	30
g2	3	3	9
g3	4	4	12
g2	3	3	9

In Galaxy we would select the following:

• Input Single or Multiple Tables → Single Table
• Column names on first row? → Yes
• Row names on first column? → Yes
• Type of table operation → Drop, keep or duplicate rows and columns
  • List of columns to select → 1,1,3
  • List of rows to select → 1:3,2
  • Keep duplicate columns → Yes
  • Keep duplicate rows → Yes

Example 2: Filter for rows with row sums less than 50

We have the following table:

.	c1	c2	c3
g1	10	20	30
g2	3	6	9
g3	4	8	12
g4	81	6	3

and we want:

.	c1	c2	c3
g2	3	6	9
g3	4	8	12

In Galaxy we would select the following:

• Input Single or Multiple Tables → Single Table
• Column names on first row? → Yes
• Row names on first column? → Yes
• Type of table operation → Filter rows or columns by their properties
  • Filter → Rows
  • Filter Criterion → Result of function applied to columns/rows
    • Keep column/row if its observed → Sum
    • is → < (Less Than)
    • this value → 50

Example 3: Count the number of values per row smaller than a specified value

We have the following table:

.	c1	c2	c3
g1	10	20	30
g2	3	6	9
g3	4	8	12
g4	81	6	3

and we want to count how many elements in each row are smaller than 10, i.e., we want to obtain the following results table:

.	vec
g1	0
g2	3
g3	2
g4	2

In Galaxy we would select the following:

• Input Single or Multiple Tables → Single Table
• Column names on first row? → Yes
• Row names on first column? → Yes
• Type of table operation → Manipulate selected table elements
  • Operation to perform → Custom
    • Custom Expression on 'elem' → elem < 10
  • Operate on elements → All

Note: There are actually simpler ways to achieve our purpose, but here we are demonstrating the use of a custom expression.

After executing, we would then be presented with a table like so:

.	c1	c2	c3
g1	False	False	False
g2	True	True	True
g3	True	True	False
g4	False	True	True

To get to our desired table, we would then process this table with the tool again:

• Input Single or Multiple Tables → Single Table
• Column names on first row? → Yes
• Row names on first column? → Yes
• Type of table operation → Compute Expression across Rows or Columns
  • Calculate → Sum
  • For each → Row

Executing this will sum all the 'True' values in each row. Note that the values must have no extra whitespace in them for this to work (e.g. 'True ' or ' True' will not be parsed correctly).

Example 4: Perform a scaled log-transformation conditionally

We want to perform a scaled log transformation on all values greater than 5, and set all other values to 1.

We have the following table:

.	c1	c2	c3
g1	0	20	30
g2	3	0	9
g3	4	8	0
g4	81	0	0

and we want:

.	c1	c2	c3
g1	1.00000000	0.1497866	0.1133732
g2	1.00000000	1.0000000	0.2441361
g3	1.00000000	0.2599302	1.0000000
g4	0.05425246	1.0000000	1.0000000

In Galaxy we would select the following:

• Input Single or Multiple Tables → Single Table
• Column names on first row? → Yes
• Row names on first column? → Yes
• Type of table operation → Manipulate selected table elements
  • Operation to perform → Custom
    • Custom Expression → (math.log(elem) / elem) if (elem > 5) else 1
    • Operate on elements → All

Example 5: Perform a Full table operation

We have the following table:

.	c1	c2	c3
g1	10	20	30
g2	3	10	9
g3	4	8	10
g4	81	10	10

and we want to subtract from each column the mean of that column divided by the standard

deviation of it to yield:

.	c1	c2	c3
g1	9.351737	17.784353	28.550737
g2	2.351737	7.784353	7.550737
g3	3.351737	5.784353	8.550737
g4	80.351737	7.784353	8.550737

In Galaxy we would select the following:

• Input Single or Multiple Tables → Single Table
• Column names on first row? → Yes
• Row names on first column? → Yes
• Type of table operation → Perform a Full Table Operation
  • Operation → Custom
  • Custom Expression on 'table' along axis (0 or 1) → table - table.mean(0)/table.std(0)

Example 6: Perform operations on multiple tables

We have the following three input tables:

Table 1

.	c1	c2	c3
g1	10	20	30
g2	3	10	9
g3	4	8	10

Table 2

.	c1	c2
g1	1	2
g2	3	4
g3	6	5

Table 3

.	c1	c2	c3
g1	1	2	3
g2	1	2	3

Note that the dimensions of these tables do not match.

Dimensions:

• Table1 [3,3]
• Table2 [3,2]
• Table3 [2,3]

In order to perform simple operations between Tables, they must be of the same dimensions.

To add Table2 to Table3 we would have to transpose one of the tables using the in-built T method:

table2 + table3.T

or:

table2.T + table3

We can also perform more general operations using all 3 tables, such as taking the minimum value of the maximum values of Table2 and Table3, and dividing the Table1 values by it:

table1 / min(table2.values.max(), table3.values.max())

To perform these types of operations in Galaxy we would select the following:

• Input Single or Multiple Tables → Multiple Tables

• (For each inserted table)

  • Column names on first row? → Yes
  • Row names on first column? → Yes

• Custom Expression →

  <insert your desired function>
  

Please note that the last example shown above was chosen to illustrate the limitations of the tool. Nested attributes like table2.values.max are disallowed in expressions in the tool so the above would have to be replaced with the harder to read workaround:

table1 / min(np.max(np.max(table2)), np.max(np.max(table3)))

Complex operations (like ones that would benefit from specifying nested attributes) can often be broken into subsequent runs ot the tool, in which the first run generates an intermediate table representing the result of the "inner" operation that the second run can then use as input to perform the "outer" operation.

Also note that, currently min(), max() and sum() are the only built-in Python functions that can be used inside expressions. If you want to use additional functions, these have to be qualified functions from the math, np or pd libraries.

Example 7: Melt

We have the following table

.	A	B	C
0	a	B	1
1	b	B	3
2	c	B	5

and we want:

.	A	variable	value
0	a	B	B
1	b	B	B
2	c	B	B
3	a	C	1
4	b	C	3
5	c	C	5

In Galaxy we would select the following:

• Input Single or Multiple Tables → Single Table
• Column names on first row? → Yes
• Row names on first column? → Yes
• Type of table operation → Perform a Full Table Operation
  • Operation → Melt
  • Variable IDs → A
  • Unpivoted IDs → B,C

This converts the "B" and "C" columns into variables.

Example 8: Pivot

We have the following table

.	foo	bar	baz	zoo
0	one	A	1	x
1	one	B	2	y
2	one	C	3	z
3	two	A	4	q
4	two	B	5	w
5	two	C	6	t

and we want:

.	A	B	C
one	1	2	3
two	4	5	6

In Galaxy we would select the following:

• Input Single or Multiple Tables → Single Table
• Column names on first row? → Yes
• Row names on first column? → Yes
• Type of table operation → Perform a Full Table Operation
  • Operation → Pivot
  • Index → foo
  • Column → bar
  • Values → baz

This splits the matrix using "foo" and "bar" using only the values from "baz". Header values

may contain extra information.

Example 9: Replacing text in specific rows or columns

We have the following table

.	c1	c2	c3
g1	10	20	30
g2	3	3	9
g3	4	8	12
g4	81	6	3

and we want to add "chr" to the elements in column 2 AND rows 2 and 4:

.	c1	c2	c3
g1	10	20	30
g2	3	chr3	9
g3	4	8	12
g4	81	chr6	3

In Galaxy we would select the following:

• Input Single or Multiple Tables → Single Table

• Column names on first row? → Yes

• Row names on first column? → Yes

• Type of table operation → Manipulate selected table elements

  • Operation to perform → Replace values

    • Replacement value → chr{elem:.0f}

      Here, the placeholder {elem} lets us refer to each element's current value, while the :.0f part is a format specifier that makes sure numbers are printed without decimals (for a complete description of the available syntax see the Python Format Specification Mini-Language).

    • Operate on elements → Specific Rows and/or Columns

    • List of columns to select → 2

    • List of rows to select → 2,4

    • Inclusive Selection → No

If we wanted to instead add "chr" to the ALL elements in column 2 and rows 2 and 4, we

would repeat the steps above but set the Inclusive Selection to "Yes", to give:

.	c1	c2	c3
g1	10	chr20	30
g2	chr3	chr3	chr9
g3	4	8	12
g4	chr81	chr6	chr3

Example 10: Pivot Table with unified Aggregator

For an input table of:

we wish to pivot the table with the 'A' column as the new row index and use the values of the column 'C' as the new column indexes, based on the aggregated values of 'D'. By default the aggregator function is the mean, but here we will instead pick the max, to yield:

In Galaxy we would select the following:

• Input Single or Multiple Tables → Single Table
• Column names on first row? → Yes
• Row names on first column? → Yes
• Type of table operation → Perform a Full Table Operation
  • Operation → Pivot
  • Index → A
  • Column → C
  • Values → D
  • Aggregator Function → max

Example 11: Pivot Table with custom Aggregrator

For an input table of:

we wish to pivot the table with the 'Position' column as the new index and transform the 'Age' and 'Random' columns to have mean and standard deviation values

In Galaxy we would select the following:

• Input Single or Multiple Tables → Single Table
• Column names on first row? → Yes
• Row names on first column? → Yes
• Type of table operation → Perform a Full Table Operation
  • Operation → Pivot
  • Index → Position
  • Column-Function Mapping
    • Value Column → Age
      • Function → mean
    • Value Column → Random
      • Function → mean
      • Function → std

This splits the matrix using "foo" and "bar" using only the values from "baz". Header values

may contain extra information.