HDgraphiX - Vahidi Lab

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

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

Type of Plot:

Horizontal Heatmap Vertical Heatmap
Woods Plot Volcano Plot Ladder Plot
3-State Comparison Peptide Uptake Plot
No Plot (Data Processing Only)

**More Info**

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 (Easiest) Choose Maximum Range and Number of Shades Smooth Gradient
Choose Colours From List and Input Bounds Input Colour Hexadecimal Values and Bounds (Most Customizable)

Number of Bound Inputs (per side):

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 6 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:

Auto Detect Bounds:

**More Info**

Manual Bounds: Lower: Upper:

**More Info**

Gradient Steps:

**More Info**

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 Consolidate States**

Consolidate States: Number of Pairs:
Keep State: ................. Merge State:

**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:
Specify Proteins to Use:

**More Info**

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:

**More Info**

Add Replicate Count to Heatmap:

**More Info**

Add Std Deviation to Heatmap:

**More Info**

Set Heatmap Row Max Length:

**More Info**
Set Heatmap Cell Size (inches): Width: Height:

**More Info**

Set Heatmap Cell Size (inches): . Match Colourbar Entry to Cell Size:

**More Info**

Woods/Ladder Plot Options

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; Set X-Axis Tick Spacing:

**More Info**

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**

Volcano Plot Options

For Volcano Plots; p-value Threshold:
For Volcano Plots; Significant Colour: Non-significant Colour:

**More Info**

For Volcano Plots; Data Point Opacity (%):
For Volcano Plots; Point Outline: Outline Colour:
For Volcano Plots; Data Point Size: Outline Width:
For Volcano Plots; Colour by Sequence Position: Gradient:
For Volcano Plots; ................. Show Colour Bar:
For Volcano Plots; ................. Gradient Steps:

**More Info**

For Volcano Plots; Set Plot Dimensions (inches): Width: Height:
For Volcano Plots; X-axis Limits: Min: Max:
For Volcano Plots; Y-axis Limits: Min: Max:

3-State Comparison Options

For 3-State Comparison; Data Point Opacity (%):
For 3-State Comparison; Quadrant Colours:

**More Info**

For 3-State Comparison; Q1 (+,+): Q2 (-,+): Q3 (-,-): Q4 (+,-):
For 3-State Comparison; Fade Colours to Neutral:

**More Info**

For 3-State Comparison; Colour Threshold:

**More Info**

For 3-State Comparison; Neutral Colour:

**More Info**

For 3-State Comparison; Point Outline: Outline Colour:

**More Info**

For 3-State Comparison; Show Diagonal Line:
For 3-State Comparison; Show Threshold Square:

**More Info**

For 3-State Comparison; Data Point Size: Outline Width:
For 3-State Comparison; Colour by Sequence Position:

**More Info**

Gradient:
For 3-State Comparison; ................. Show Colour Bar:
For 3-State Comparison; ................. Gradient Steps:

**More Info**

Peptide Uptake Plot Options

For Peptide Uptake Plots; Connect Data Points:
For Peptide Uptake Plots; Set Plot Dimensions (inches): Width: Height:
For Peptide Uptake Plots; Y-axis Limits: Min: Max:
For Peptide Uptake Plots; Log Scale X-axis:
For Peptide Uptake Plots; X-axis Limits: Min: Max:
For Peptide Uptake Plots; Show Grid Lines:
For Peptide Uptake Plots; Data Point Size:
For Peptide Uptake Plots; Point Outlines: Outline Width:
For Peptide Uptake Plots; State Colours: Number of States:
For Peptide Uptake Plots; State Name: ................ Colour: .. Outline Colour:

Pulse Labelling Options

For Pulse plotting; State of Interest:

**More Info**

For Pulse plotting; Reference Time:

**More Info**

For Pulse plotting; Number of time points:
For Pulse plotting; Time Points:

**More Info**

RFU/Absolute Uptake Options

For RFU plotting; Multiply Values by 100:

**More Info**

for RFU plotting;. Use Absolute Uptake Values:

**More Info**

Colouring Script Options

For Colouring Scripts; Chain Dictionary: Number of Proteins:

**More Info**

For Colouring Scripts; Protein: ......................... Chain ID:

For Colouring Scripts; Peptide Visibility Priority:

**More Info**

For Colouring Scripts; Default Maximum Uptake Minimum Uptake

Input DPI for image:

**More Info**

Generate PDF rather than PNG:

**More Info**

Select if you wish to download PyMOL colouring scripts:

**More Info**

Select if you wish to download ChimeraX colouring scripts:

**More Info**

........ See Advanced Options to specify structural chains to colour with these scripts

Include replicate count and std deviation CSV (state comparisons):

**More Info**

Include replicate count and std deviation CSV (per state):

**More Info**