RDML-BarGraph

Create bar graphs for publication.

Get help · RDML-Tools · Source
Load table file



Table after import




Combine Data:




SVG vector files can be adapted to individual needs or converted to PNG/JPG using Inkscape (click to download).





Y-Axis
Image Scale:
Max Y Value:
Min Y Value:
Axis Line Strength:
Tick Line Strength:
Tick Line Length:
Space to Text:
Text Size:
Font Type:
Description:
Space to Desc.:
Desc. Size:
Desc. Type:



X-Axis
Empty Space for Missing Bars:
Gap Width between Bars:
Gap Width between Groups (additional):
Axis Line Strength:
Tick Line Strength:
Tick Line Length:
First Order:
Rotate Axis Text:
Space to Text:
Text Size:
Font Type:
Space to Group Line:
Group Line Strength:
Group Line Extension:
Second Order:
Rotate Axis Text 2:
Space to Text 2:
Text 2 Size:
Font Type 2:



Box Plot
Box Line Strength:



Error Bars
Show Error Bars:
Error Bars Shape:
Tick Line Strength:
Tick Line Length:



Datapoint Dots
Show Individual Dots:
Dot Placing Method:
Dot Size:
Dot Line Width:
Dot Color:



Graph Basics
Height:
Width:
Image Scale Unit:
Title:
Space to Title:
Title Size:
Title Type:

Application Description

RDML-TableShaper is a tool to shape tables with amplification data for the import with RDML-tools. This is error-prone and second best to original RDML export by the machine. As some machines do not offer RDML export, TableShaper might help. Most qPCR machines export Excel files. Please convert them by opening in Excel (Microsoft) or Calc (Libre Office), selecting the table with the amplification data and save as tab separated text file. The tab separated text file can be modified using TableShaper.

Function to place the dots

The function to place the dots in a not overlapping form was heavily inspired by the calculateCompactSwarm function from the R package beeswarm (see https://github.com/aroneklund/beeswarm).

The use of TableShaper

TableShaper follows three consecutive steps:

1. The table separators have to be identified on the first tab. If it does not work out automatically, the separator has to be selected manually. The table columns need to be recognized in the table below.

2. The content need to be recognized in the second tab. If your table format is not found in the predefined settings, you may iteratively select the parameters and load / save them for later use. Adapt the "Number of columns to keep" and "Number of rows to keep" to match the experiments cycle and well numbers and avoid cutoff. "Settings to reshape the table" is the most dramatic shaping option. You can opt to flip the table or to build a table from value list. The result is drawn below and can be used to select the columns for data extraction.

3. Fill the missing content in the third tab. To be able to import the table into RDML, the first six columns have to be filled. Using the fields on the third tab eases this step as squares B2-D7 can be used. Take care in this step as errors in the target id and sample id can not be fixed in RDML later. Save the result as .tsv file.

4. To create an RDML file fill the information on the "Create RDML file" card and hit the button. RDML-Edit will open with the created RDML file and allow to save or view the RDML file.
Alternatively the data can be imported int existing RDML files. Open the RDML file in RDML-Edit (or create new) and enable editing with the "enable edit mode" button. Now change to the experiments tab and open an experiment or create a new experiment. In the experiment, create a new run. Take care to set the ID and PCR-Format fields correctly. Now select the exported .tsv file in "Import Amplification Data". Once saved you can inspect the result using RunView or save it as RDML file on the first tab.

Accepted Input

The table files can be provided in text format with tab, comma or semicolon as separator(*.txt, *.tsv, and *.csv).

Sample Data

The "Show Example" button loads an example table file (click to download file) from a BioRad iCycler v9.35.

More Help

A general help file is available as RDML-Tools Help.