Basic statistics

constant operator

Description

constant operator allows for a value equal to a constant to be generated

Usage

Input projection	.
none

Input parameters	.
value	numeric, the constant value to be generated, default is 0

Output relations	.
constant	numeric, one constant is generated per cell

Details

A constant value is generated for all the data. All factors are therefore associated with this constant. A typical use of this operator is when you require to generate fixed boundary values to be used as a grid line in a later (i.e. downstream) step. The grid line is created in a layer using the h-grid view type. An example would be to create a zero grid line, where theconstantoperator is used to generate a zero value and a zero line is then available for later visuals.

References

See Also

Examples

https://tercen.com/operator/p/8d8febb97ed4b09c2ddf52795c961e68

GitHub link

constant_operator on GitHub

count operator

Description

count operator counts the number of data points.

Usage

Input projection	.
y-axis	is the input data to be counted, per cell

Output relations	.
count	numeric, count of the input values

Details

The operator takes all the values of a cell and counts them. The computation is done per cell. There is one value calculated and returned for each of the input cell.

References

See Also

product, sum

Examples

GitHub link

count_operator on GitHub

cv operator

Description

cv operator calculates the coefficient of variance on a set of input values.

Usage

Input projection	.
y-axis	values to be used for the calculation of the cv, per cell

Output relations	.
cv	numeric, coefficient of variation result per cell

Details

The coefficcient of variation is a measure of variaton, it is equivalent to standard deviation divided by the mean.

cv = sd/mean

The cv is returned as a fraction.

References

see the https://en.wikipedia.org/wiki/Coefficient_of_variation

See Also

sd, mean

Examples

GitHub link

cv_operator on GitHub

density operator

Description

density operator performs a density caculations on x and y input values.

Usage

Input projection	.
x-axis	indicates the values of the x
y-axis	indicates the values of the y

Output relations	.
density	numeric, density calculation, calculated per cell

Details

A density calculation is performed per cell with the input values defined by the x and y-axis, the result are density values associated with each cell. The density operator is typically used in a pairwise plot and the returned density values are usually used as a coloring in a pairwise plot of the original input values.

References

See Also

Examples

GitHub link

density_operator on GitHub

foldchange operator

Description

foldchange operator performs a fold change (i.e. ratio) caculation between two values.

Usage

Input projection	.
x-axis	contains the grouping factor for the fold change calculation,
y-axis	values

Input parameter	.
reverse	logical, to reverse the calculation, default is FALSE

Output relations	.
FoldChange	numeric, foldchange, calculated per cell

Details

A foldchange operation is performed per cell. Each cell has values defined by the y-axis and seperated by the x-axis. The result of the foldchange is the ratio of the first divided by the second. If reverse is selected then the order of the ratio is changed.

References

See Also

ratio,logfoldchange ##### Examples

GitHub link

foldchange_operator on GitHub

IQR operator

Description

The IQR operator returns the interquartile range of a set of data points.

Usage

Input projection	.
y-axis	numeric, input data, per cell

Output relations	.
iqr	numeric, median of the input data

Details

The operator takes all the values of a cell and returns the IQR value. The computation is done per cell and a single value is returned for each of the input cell.

References

https://en.wikipedia.org/wiki/Interquartile_range

See Also

mean_operator sd_operator cv_operator

GitHub link

IQR_operator on GitHub

logfoldchange operator

Description

logfoldchange operator performs a fold change (i.e. ratio) caculation between two values.

Usage

Input projection	.
x-axis	contains the grouping factor for the log2 fold change calculation,
y-axis	values

Input parameter	.
reverse	logical, to reverse the calculation, default is FALSE

Output relations	.
logFC	numeric, logfoldchange calculated per cell

Details

A logfoldchange operation is performed per cell. Each cell has values defined by the y-axis and seperated by the x-axis. The result of the logfoldchange is the log2 values where of the first is substrated by the second. If reverse is selected then the order of the substraction is changed.

References

See Also

ratio,foldchange ##### Examples

GitHub link

logfoldchange_operator on GitHub

max operator

Description

max operator returns the maximum of a set of data points.

Usage

Input projection	.
y-axis	numeric, input data, per cell

Output relations	.
max	numeric, max of the input data

Details

The operator takes all the values of a cell and returns the value which is the maximum. The computation is done per cell (one value is returned for each input cell).

References

Based on the max R function.

See Also

product_operator, sum_operator

GitHub link

max_operator on GitHub

Mean imputation operator

Description

mean_imputation operator replaces missing values by the column mean.

Usage

Input projection	.
row	factor, observations
column	factor, variables
y-axis	numeric, input data, per cell

Output relations	.
mean_imputed	numeric, measurements with imputed values

Details

The operator replaces missing values (NA) by the column mean.

References

See Mean substitution on Wikipedia.

See also

impute_operator

GitHub link

mean_imputation_operator on GitHub

mean operator

Description

mean operator computes the mean of a set of data points.

Usage

Input projection	.
y-axis	is the input data for the mean, per cell

Output relations	.
mean	numeric, mean of the input values

Details

The operator takes all the values of a cell and calculates their mean. The computation is done per cell. There is one value calculated and returned for each of the input cell.

References

See Also

product_operator, sum_operator

Examples

GitHub link

mean_operator on GitHub

mean sd operator

Description

mean sd operator computes the mean and standard deviation of a set of data points.

Usage

Input projection	.
y-axis	numeric, input data, per cell

Output relations	.
mean	numeric, mean of the input data
sd	numeric, standard deviation of the input data

Details

The operator takes all the values of a cell and calculates their mean and standard deviation. The computation is done per cell. There are two value calculated and returned for each of the input cell.

References

See Also

product_operator, sum_operator

Examples

GitHub link

mean_sd_operator on GitHub

Median operator

Description

Median operator returns the median of a set of data points.

Usage

Input projection	.
y-axis	numeric, input data, per cell

Output relations	.
median	numeric, median of the input data

Details

The operator takes all the values of a cell and returns the value which is the median.The computation is done per cell. There is one value returned for each of the input cell.

References

See Also

mean_operator ##### Examples

GitHub link

median_operator on GitHub

negative operator

Description

negative operator performs a negative of values

Usage

Input projection	.
y-axis	values to be negated

Output relations	.
negative	numeric, negative per data point

Details

A negative of values is performed.

References

See Also

Examples

GitHub link

negative_operator on GitHub

Pairwise RMSD operator

Description

The pairwise_RMSD operator returns the Relative Mean Squared Deviation computed between pairs of variables.

Usage

Input projection	.
row	factor, input variables
col	factor, observations
.y	numeric, measurements

Output relations	.
rmsd	numeric, RMSD
to	numeric, variable to be projected against the initial one for pairwise distance visualisation

Details

References

See Also

Examples

GitHub link

pairwise_RMSD_operator on GitHub

pearson operator

Description

pearson operator performs a person correlation of two input sets of data per cell

Usage

Input projection	.
x-axis	value of one group of data
y-axis	value of other group of data

Output relations	.
cor	numeric, pearson correlation calculated per cell
pv	numeric, p-value calculated per cell

Details

A pearson correlation is performed per cell where the two groups of data to be correlated are found on the x-axis and y-axis. This operator is ideally suited as an operator for multiple pairwise projections in Tercen.

References

see the base::cor.test function of the R package for the documentation,

See Also

Examples

GitHub link

pearson_operator on GitHub

Percentile operator

Description

percentile operator returns the percentile of a set of data points.

Usage

Input projection	.
y-axis	numeric, input data, per cell

Input parameters	.
percentile	numeric, the percentile to use, default is 0.01, 1% percentile

Output relations	.
percentile	numeric, percentile of the input data

Details

The operator takes all the values of a cell and returns the precentile value. The computation is done per cell. There is one value returned for each of the input cell.

References

See Also

product_operator, sum_operator

Examples

GitHub link

percentile_operator on GitHub

Introduction

This is a template repository.

Use this template repository during the first step of developing a tercen operator (in R) on github.

An overview of steps for developing an operator are:

1. create a github repo
2. install tercen_studio
3. login to tercen_studio
4. git clone the newly created repo
5. start developing in R in tercen_studio
6. add R packages to the repo
7. push to the github repo
8. go to tercen and install the operator

For step 1, when creating the repo on github, you will notice the option to use a template repository, choose the templateR_operator repository and select it as the template repository.

After creation, you now have a new repository with all the convenient files for making a new operator (in R) for tercen.

Use tercen_studio to clone the new repository and start programming in tercen_studio

it includes the skeleton files

• main.R
• workspace.R
• operator.json
• README_template.md
• doc directory

please remember to change the README_template.md to README.template.md

inside the doc there is a dev_commands.md file which contains useful development command lines.

GitHub link

read_VCF_operator on GitHub

RMSD operator

Description

RMSD operator returns the Relative Mean Square Deviation of two variables.

Usage

Input projection	.
x-axis	numeric, input data, per cell
y-axis	numeric, input data, per cell

Output relations	.
rmsd	numeric, RMSD of the input data

Details

References

See Also

lm_operator

Examples

GitHub link

RMSD_operator on GitHub

Sample operator

Description

Sample operator returns a sample of the specified size from the set of data points using either with or without replacement.

Usage

Input projection	.
y-axis	numeric, input data
cols	numeric, observations, the sample factor(s)

Input parameters	.
size	numeric, the fraction to sample, default is 1 (100% percent)
replace	boolean, should replacement be used? , default is false (no replacement)

Output relations	.
sample	numeric, sample of the input data

Details

The operator randomly selects columns (i.e. samples)

References

See the sample function in base R.

See Also

Examples

GitHub link

sample_operator on GitHub

scale operator

Description

scale operator performs a scaling of the data

Usage

Input projection	.
row	represents the variables (e.g. channels, markers, genes)
col	represents the observations (e.g. cells, samples, indviduals)
y-axis	measurement value

Input parameters	.
scale	logical, if scale is TRUE then scaling is done by dividing the (centered) row of x by their standard deviations if center is TRUE, and the root mean square otherwise. If scale is FALSE, no scaling is done.
center	If center is TRUE then centering is done by subtracting the row means (omitting NAs) of x from their corresponding columns, and if center is FALSE, no centering is done.

Output relations	.
scale	numeric, per cell

Details

The operator is the scale function in base R.

References

See the base::scale function of the R package for more details.

GitHub link

scale_operator on GitHub

sd operator

Description

sd operator computes the standard deviation of a set of data points.

Usage

Input projection	.
y-axis	is the input data for the sd, per cell

Output relations	.
sd	numeric, sd of the input values

Details

The operator takes all the values of a cell and calculates their standard deviation. The computation is done per cell. There is one value calculated and returned for each of the input cell.

References

See Also

mean_operator, sum_operator

Examples

GitHub link

sd_operator on GitHub

Seqlen operator

Description

Seqlen operator creates a sequence annotation for a data series

Usage

Input projection	.
y-axis	numeric, input data, per cell
x-axis	numeric, input data, ordering of the data series

Output relations	.
seq	numeric, sequence of the input data

Details

The operator takes all the values of a cell ordered by the ’x-axis’and gives a sequence number to each data point in the cell.

References

See Also

topn_operator

Examples

GitHub link

seqlen_operator on GitHub

Shift operator

Description

shift operator performs a shift by a constant value.

Usage

Input projection	.
y-axis	values as input to the shift operator

Input parameters	.
constant	numeric, the shift value, default is 0

Output relations	.
shift	numeric, output shift transformation per data point

Details

A shift by a constant value is performed to all data points.

value + shift

References

See Also

Examples

GitHub link

shift_operator on GitHub

signchange operator

Description

signchange operator negates the data value, i.e. sign changes

Usage

Input projection	.
y-axis	value of data to be sign changed

Output relations	.
signchange	numeric, the opposite sign of the value

Details

The sigchange operator changes the sign of the data by negating the value.

References

See Also

Examples

GitHub link

signchange_operator on GitHub

topn operator

Description

topn operator returns data points.

Usage

Input projection	.
y-axis	numeric, input data, per cell

Output relations	.
elements	numeric, choosen elements of the input data

Details

The operator takes all the values of a cell and returns the top n elements.

References

See Also

Examples

GitHub link

topn_operator on GitHub

Upper and lower bounds operator

Description

upperandlowerbounds operator computes an upper and lower bound values as a fraction of a given data point.

Usage

Input projection	.
y-axis	is the input data for the multiplication per cell

Input parameters	.
fraction	numeric, fraction value
percentage	boolean, the relative values are returned as percentages

Output relations	.
upperbound_absolute	numeric, upper absolute bound value
lowbound_absolute	numeric, lower absolute bound value
upperbound_relative	numeric, upper relative bound value
lowbound_relative	numeric, lower relative bound value

Details

The operator takes the mean value of a cell and calculates an upper bound and a lowerbound. The computation is done per cell. There are four values colculated and returned for each of the input cell.

The operator takes the mean value and calculates an upper bound by adding to it

  upperbound_absolute = value + (value * fraction)
  lowerbound_absolute = value + (value * fraction)
  
  upperbound_relative = (value * fraction)
  lowerbound_relative = (value * fraction)

Use this operator when wanting to determine upper and lower bounds. These generated bounds are usually used in a downstream data step for a graphics representation using grid lines which correspond to the boundary values (see horizontal grid lines feature)

GitHub link

upperandlowerbounds_operator on GitHub

Word count operator

Description

Word count operator count the occurences of each words in one or more documents.

Usage

Input projection	.
row	is the documentId

Output relations	.
count	numeric, mean of the input values
word	character, the word
documentId	character, the id of the document

Details

The operator count the occurences of each words in one or more documents.

References

See Also

Examples

GitHub link

wordcount_operator on GitHub