HDgraphiX - Vahidi Lab

File Upload:
DynamX Cluster HDExaminer HDX Workbench
Upload as .csv File:

Type of Experiment:
Continuous Labelling - State Comparison
Relative Fractional Uptake
Absolute Deuterium Uptake

Type of Plot:

Horizontal Heatmap
Vertical Heatmap
Woods Plot Volcano Plot
Ladder Plot

Store Values:

**More Info**

Download settings .csv file:
Upload settings .csv:
Use Uploaded Settings:

Font Choices:
Font Size:

Title Size:

Tick Label Size:

Font:

Font Colour:

Choose Bounds/Colours Input Type:
Automatically Set Range Based on Data (Easiest) Choose Maximum Range and Number of Colour Shades
Choose Colours From List and Input Bounds Input Colour Hexadecimal Values and Bounds (Most Customizable)

Set Range and Shades

Maximum Range:

Number of Shades:

Choose Colours:

Negative Values:
Positive Values:

Input Bounds: **More Info**

Negative bounds:

Positive bounds:

The data range will be determined by the maximum absolute value in the provided data, with 7 shades of colours.

Please input colours as hexadecimal values, beginning with a pound sign (eg. #FFFFFF)
Input Darkest Colour Values Input All Colour Values

Input Colours:

Input Darkest Colour for Negative Values:

Input Darkest Colour for Positive Values:

Input Colours:
Note: Each colour list (pos/negative) should be 1 shorter than each bound list (pos/negative), and not include white (#FFFFFF) which will be added.
This is not true if Colour Insignificant is chosen in Advanced Options, if this is chosen the lists should be equal length to the list of bounds.

Input Darkest Negative Colour to Lightest Negative Colour:
▪ □

Input Lightest Positive Colour to Darkest Positive Colour:
□ ▪

Input Bounds: **More Info**

Negative bounds:

Positive bounds:

Click Here for Advanced Options

Select boxes next to desired Advanced Options

**How to use Change Bounds**

Change Bounds:
Positive Negative Both
Global Maximum:

**How to use the Drop Times Option**

Drop Times: Number of Timepoints to Drop:

**How to use the Drop Peptides Option**

Drop Peptides: Number of Peptides to Drop:
Protein Name: ............... Start Residue: ............... End Residue:

**How to use the Drop Proteins Option**

Drop Proteins: Number of Proteins to Drop:

**How to use Renumbering**

Renumber Residues: Number of Proteins to Renumber:
Protein: ......................... Value:

**How to use Domain Labelling**

Labelling Domains: Number of Domains to Generate:
Domain Name: .............. Start Peptide: ................ End Peptide: ................. Colour:

Don't Have Mutants Mutants in Data

**How to use the Mutation ID Dictionary**

Mutation ID Dictionary: Number of Point Mutations:
Mutant Protein ID: ......... Wild Type Protein ID: .... Residue Number: .......... Desired WT Residue:

Compare Everything Select States to Compare

**How to use the State Lists**

Number of Comparisons:
State List 1: ................. State List 2:

Colour Insignificant Values (Not White):

**More Info**

Separate Heatmap Plots:

**More Info**

All Time Labels in One Unit:

**More Info**

Change Title Padding: Title: Subtitles:

**More Info**

Change Titles: Plot Title:
Change Titles: X-Axis Title:
Change Titles: Y-Axis Title:

Change Default Colouring:

**More Info**
Change Neutral Cell Colour (White Cells):
Change Colour for Cells Lacking Data:
Please input colours as hexidecimal values beginning with a pound sign

Heatmap Cell Dividing Colour/Thickness: Colour: Thickness:

**More Info**

Change State Comparison Separating Line: Colour: Thickness:

**More Info**

Change Heatmap Border: Colour: Thickness:

**More Info**

Change Heatmap Ticks: Tick Colour: Label Colour: Width: Length:

**More Info**

Add Cell Values to Heatmap:
Set Heatmap Row Max Length:

**More Info**

For Woods/Ladder Plots; Colour Gradient According to Heatmap:

**More Info**

For Woods/Ladder Plots; Set Plot Dimensions (inches): Width: Height:
For Woods/Ladder Plots; Change Peptide Thickness: Colour Thickness: Border Thickness:

**More Info**

For Woods/Ladder Plots; Set Colour Cutoff Value (Woods):

**More Info**

For Woods/Ladder Plots; Set Colours (Woods): Negative: Near Zero: Positive:

**More Info**

For Woods/Ladder Plots; Remove Horizontal Threshold Markers (Woods):

**More Info**

For Woods/Ladder Plots; Change Y-Axis Determination (Woods):

**More Info**

For Woods/Ladder Plots; Flip Y Axis (Ladder):

**More Info**

For Volcano Plots; p-value Threshold:
For Volcano Plots; Set Alternate Point Colour: