BM432 Data Visualisation Workshop

Morgan Feeney

University of Strathclyde

Leighton Pritchard

University of Strathclyde

2026-10-21

1. Introduction

Learning Objectives

  • You should be able to critically analyse how data is visualised
  • You should be able to judge a figure’s clarity and potential for misunderstanding
  • You should be able to identify potential sources of bias resulting from the visualisation
  • You should understand how to create effective figures for your own work

2. Critique of Published Scientific Figures

Example 1

Figure 1: Small molecules identified in previous HTS increase GCase activity.

Your Critical Analysis of Example 1

Your Critical Analysis of Example 1

Reasons for the grade
included statistics and attempted to use colour consistently
They have clearly presented their data, included descriptions of each figure in the legend, including the statistical testing, significance (p-values), figures labelled appropriately and they have used colours for more clarity and differentiation of the groups.
the figure was clearly labelled, headings, statistical tests. the figure ledged was easy to follow and clear. colours are coordinated and remain consistent throughout all figures. statistical test results seem appropriate
The figures are visually attractive, ordered correctly.
The error bars, axis labels and values are clear and consistent
Clear diagrams and informative figure legend which are easy to interpret but there are some visual inconsistencies across panels.
nice layout, easy to follow along
its nicely laid out but bad for colourblind people
The figure presents the results clearly using different graphs & microscopy images, with appropriate statistical information. however, some panels are looking overcrowded and the small labels and multiple significance comparisons make the results difficult to interpret.
Very visually appealing, clearly depicts all points its trying to get across in a cohesive and easy to read manner. Figure legend is clear and comprehensive.
logical flow of the panels
Clear and easy to follow
Good flow, consistent colour scheme, appropriate statistical analysis, easy to understand and see key differences in the results.
The figure flows and is easy to follow, good colour scheme (consistent), stats seem correct and significance is on there, easy to understand/see key differences in results
colour representation across concentrations are too similar making it less clear at a glance, brief but clear explanations of each graph, no explanation of abbreviations, clear show of sgnificance and clear/concise graphs
without explanations of what the abbreviations mean, it is very difficult to understand what it is this person is referring to, however, the figures are otherwise clear with a good font, statistics are well represented in the figure and legend.
the figures are easy to read, nicely labelled and well presented.
The figure presents multiple lines of evidence, including chemical structures, quantitative data, and representative microscopy images, which together support the study’s conclusions. However, the presentation is visually cluttered, several labels and text are difficult to read, and the statistical and imaging data could be displayed more clearly to improve interpretation and publication quality.
Whilst at first glance this looks like a good visual figure, however, figure 1B has so many significance bars all crossing over each other making it difficult to read, figure 1C & F have no x-axis labels about the magnification used to take the microscopic images and there is no data presented for A18 in 1G.
Great flow of images which transitions, telling a story from one to another. Clear statistics and detail given.
Structure of molecules were relevant. Right statistical test were performed. 3 technical replicant were used p value was mentioned. But few statistical data was missing.
Figure and legend communicate findings effectively, but improvements for clarity and reproducibility could be made
Clearly labelled with the colour palette aiding in the labelling.
The figure presents a broad set of complementary evidence, combining chemical structures, quantitative activity measurements, microscopy, and statistical annotations. However, the dense multi-panel layout, limited display of individual observations, and reliance on significance stars reduce clarity.
Effective multi-panel figure. Appears to tell a story. Inclusion of chemical structures is useful. Use of different techniques gives a full picture. Statistical analysis is well represented.
There are minor flaws in the details, some small errors in certain sections, and insufficient visual appeal, but overall readability is acceptable.
This set of charts is systematic and can reflect the conclusion.
Good level of detail included and layout is alright. however, the figure seems slightly crowded making it harder to follow but detailed figure legend helps to explain the figure. bar charts easy to follow
The data is clearly described in the legend however panels C and F are a bit more difficult to visualise due to the lack of contrast for the DAPI and TFEB and the merged image doesn’t clearly show the overlaps. Aside from this, the figures are clearly labelled with stats and the colour coding is consistent across the panels.
Excellent graphs
The figure uses several methods and has a detailed legend but seven panels make it crowded and some results are difficult to interpret
Overall very good but personally slightly mislead by certain colours between panels
The figure combines quantitative measurements with representative microscopy images, allowing the findings to be assessed using complementary forms of evidence
Clear stats, good notation, clear figure legend
bar charts appropriately labelled and easy to interpret
no comprasion between a16 & a18; hard to see clear comparisons in figure e
Good use of white space and colour for clarity. Some data measurements aren’t clear based on the figure description, statistical analysis is appropriate for data

Your Critical Analysis of Example 1

Suggestions for improvement
Too much text on the graphs, figure B) is too busy, say how many replicates were used and specify whether they are technical or biological
However, they need more clarity as I did not understand what they were testing e.g. what is A16 and A18. They could also improve the layout of their panels, as the bottom row looks a bit cramped, so need better use of white space.
a lot of bar charts, maybe another figure type could have been used? i’m unsure if the type of statistical test is obviously stated
In B it isnt clear why they just statistically compare each result to the first bar, seems incorrect. Similarly in graph E, the comparison of P values doesnt appear to make sense
colour blind people may struggle
change colours and add more space
The figures could be made a little larger with clearer labels and less crowded statistical comparisons. Individual data points to the bar charts would also help show the variation between replicates.
lots of different things going on could be maybe split into different figures.
Could they be split? lot of panels doing different things for one figure
they could have used less similar shades of colours to show concentration differences especially for A18 as the 2 lower concentrations look basically the same
Could potentially be better if the panels were separated more clearly, maybe by boxes or another colour. also again, clarifying the abbreviations
Increase the font size and readability of axis labels, statistical annotations, and panel labels. Replace the bar chart with a dot or box plot to show individual data points and data distribution, include sample size (n) and define the error bars, and provide quantitative analysis of the microscopy images rather than relying solely on representative images. Improved alignment and spacing between panels would also reduce visual clutter and enhance clarity.
- For 1C and 1F add x-axis that details the level of magnification used
  • Add in data to1G/not include in final results if the experiment was not finished
  • For 1B change the type of graph used to present as error bars are not clear and the correlations between the different significance levels for each group are hard to understand.
  • Keep consistent colour key across all figures (e.g. 1uM concentration green same throughout) | |Very densely packed which can be confusing to read let alone analyse. Panel B especially has overlapping significance brackets, and the rotation of X axis samples makes it harder to read. | |Concentration of DMSO is not cleared. No statistical difference between the A16 and A18 has been showed; in panel B. Immunofluorescence confocal microscopy intensity value wasn’t mentioned. panel D is also missing statistical difference of A16 and A18 therefore we don’t know if both equally influence TFEB nuclear localization in Hela cells? | |The figure could be split up, as there are many panels crammed into one figure. | |Show individual data points alongside bars and error bars, especially because some experiments have small sample sizes. Report exact p-values and clearly state the sample size for each quantitative panel. Clarify the normalization in panels B and E, including what “% vehicle” represents. Reduce visual crowding, particularly in panel E, where labels and treatment groups are difficult to read. Use more consistent colour coding for A16 and A18 across all panels and ensure the palette is colour-blind accessible. | |The colours between bars are very similar, which could prove difficult for those with accessibility issues. There is a lot of information on each graph with small font, making it less clear. | |Some tables can be styled differently, and colors can also be improved. | |The picture notes are not clear | |spacing between sections of figures could be slightly wider | |It could be improved by including the coloured microscope images before merging | |make labels larger, improve spacing, show individual data points and state the exact sample sizes | |Using the same colour between panels for different concentrations is a bit confusing. | |The figure is a little bit crowded, with seven panels and small labels, making the experimental results and statistical comparisons difficult to interpret quickly. | |More statistical analyses for comparisons of confocal microscopy | |statistical test for graph B not listed, quantification method for figure B and D not stated and scale bar for microscopy image not shown | |Clearer descriptions for data beyond quantification |

Critique 1.1

Issue

Dynamite plot: the lower extent of these error bars is not visible.

Solution

Use boxplots or 1D scatterplots

Critique 1.2

Issue

Incomplete presentation of statistical comparisons, e.g is there a difference between A16 and A18 in (B)?

Solution

Present a table of statistical differences instead, or alongside the figure.

Critique 1.3

Issue

Distance between bars makes comparison awkward.

Solution

Place things to be compared by the reader next to each other where possible, to facilitate visual comparison.

Critique 1.4

Issue

The scale on the micrographs (especially in panel C) is too small to read easily.

Solution

Increase the size of the scale relative to the figure so it can be read.

Critique 1.5

Issue

A visual control (bright-field image) is absent.

Solution

In addition to showing DAPI and immunofluorescence images of the cells, include a bright-field micrograph of the cells (no fluorescence).

Critique 1.6

Issue

The colour scheme is misleading because saturation represents different data across figure panels (compare 1 \(\mu\)M A18 in B vs 5 \(\mu\)M in D, and 1 \(\mu\)M A18 in E).

Solution

Be consistent with the visual messaging of colour (hue, saturation, and luminance).

Critique 1.7

Issue

Too many comparisons in B clutter the figure and compress the space available for showing data.

Solution

Present a table of statistical differences instead, or alongside the figure, to reduce clutter.

Critique 1.8

Issue

\(y\)-axis scales vary between panels, so quantitative comparison between panels is difficult.

Solution

Use the same \(y\)-axis scale in all panels to facilitate direct comparison.

Our Critical Analysis

Post-survey results

Example 2

Figure 2: Endometriosis-associated macrophages exhibit significant transcriptomic heterogeneity.

Your Critical Analysis of Example 2

Your Critical Analysis of Example 2

Reasons for the grade
Good attempt at explaining workflow of experiments, each figure is a bit too busy
They have clearly stated what they are investigated and it follows along nicely in Figure 1a. They state what each abbreviation stands for.
very colourful.
I feel like the layout of the figures isn’t making sense, it feels a bit ‘messy’.
However when you focus on each one individually they do make sense and seem clearer. I like how they have used different methods of data analysis
Poor presentation of material and poor figure legend for the figure.
detailed but very busy and hard to follow along
alot of detail but so much going on hard to read, especially C and D
The figure provides a detailed presentation of the results using different graphs & colour coding to show the macrophage populations. However, the figure is crowded and the small labels and complex heat map make some of the results difficult to read/understand.
Visually appealing but not as easy to for me to parse as the other examples, especially concerning figures C and D.
too much info - maybe better split up into a few different figures
Good but harder to follow
Hard to follow, panel B is very spread out, there is methods as well as results in the same figure. Figure legend is not very clear, e.g. panel D is supposedly top 5 genes but I cannot understand what the top 5 actually are. There’s is no statistical analysis.
Does not really tell a story of what is going on? hard to follow, too much going on, why is there a diagram of work flow in with results? even visually panel B is spread out in a way you cant really read. figure legend is not descriptive in a way that allows you to understand. colour scheme is eye catching and alone with more detailed explanations each panel could be okay?
data is confusing, clustered together and not very clear at times but some are presented well. some labelling is too small and crushed together to read.
fonts appear a bit inconsistent with some bold and some not. no titles on the actual panels. some panels don’t mention the techniques used to investigate what is being shown in the panel (e.g C).
the colours used in the graph somehow makes it difficult to read and understand.
This figure effectively combines a workflow schematic, UMAP clustering, sample composition analysis, heatmaps, and feature plots to communicate transcriptomic heterogeneity across macrophage populations. The visualisations are scientifically appropriate and provide strong data integration, although the figure is information-dense and some labels are difficult to read at publication size.
Found it difficult to read and understand, without reading the figure legend and the rest of the paper you would not be able to answer easily what the findings from this data would be.
Appealing imagery at first glance to many audiences, and comprehensive RNA sequencing pipeline.
This figure was chaotic.
Well structured, clearly labelled, however quite cluttered and legend could be slightly better defined
Clear panels with good spacing, clear heat map
The figure combines workflow, UMAP clustering, sample composition, gene-expression heatmaps, and feature plots into a coherent biological narrative. However, the dense layout, many colours, small labels, and difficult-to-compare stacked bars make detailed interpretation challenging.
Quite difficult to interpret. A lot of information in one figure. Workflow is beneficial to envision. Figure legend is helpful for more visualisation. Not entirely sure what I am supposed to understand.
The font is too small, the colors are chaotic and unattractive, making it difficult to read.
The color and text annotation make the whole picture very clear at a glance and have a good visual effect.
very hard to follow in the top part of the figure as sections A-C seem to be crammed together, making it hard to see what is part of what. figure legend helps clarify dome of the figure
There is a lot of detail in this figure, however the structure could do with some work.
What does Figure2C’s color represent? Confusing diagram
the figure uses several useful graphs to show differences between macrophages but some panels are complex and difficult to interpret
individual elements look good and the overall figure is comprehensive, layout needs work
Manages to display the results from several different techniques efficiently but i found it hard to read and extract information
Good figures, visuak representation, hard immediatately figure out which Letter corresponds to which figure
- schematic too vague
  • layout confusing, specifically how B and C is formated
  • headings for sub figures needed for clarity
  • figure C, label axis for clarity
  • figure D text is hard to read
  • figure E, label plot, confusing | |too small; bad color matching | |Clear progression from experiment design to results. Appropriate visualisation of single cell transcriptomics, library based clustering rules out technical variation |

Your Critical Analysis of Example 2

Suggestions for improvement
remove the map above part C and move the colour key closer to the figure. Also organise the CD45 cell subsets in a way that its easy to interpret (eg all blue at the bottom of the chart. Add colour key to heat map.
The layout of this figure is very bad, as they overlap on top of each other, it is very crowded, some of the text is not even readable (at least for me) and the colour scheme is so confusing. I don’t think there is enough information in the legend to understand what’s going on in each figure. It looks visually like a headache and they don’t have any statistical analysis, data analysis or statistical testing (although, I’m not sure how you can with this type of data).
very busy. a lot of pictures, very confusing to look at. confused as to what some of them show
I feel like the figure legend could maybe go into a little bit more detail onto what the data is representing, especially for C.
Make the schematic of workflow clearer, add arrows or numbers between steps. Make your figure legend clearer. Consider spacing out and defining panels so they are not overlapping one another.
D - very hard to read and understand
redo C and D
The figure could be improved by increasing the font size & simplifying the heat map to show important results. Using consistent colour scheme across the panels can also help to make the figure easier to compare the different macrophage populations.
Split the methods and results into 2 separate figures. Maybe make panel D its own panel and explain it more highlighting important differences. Do statistical analysis.
Could there have been an easier visual to display this? D) is this the top 5 like the legend says? No statistical analysis
better spacing and labelling/descriptions
could also be improved by breaking up some of the white background with boxes as hard to tell where one panel ends and another begins.
The figure contains a large amount of information, making it challenging to interpret quickly. Increasing font sizes, simplifying cluster names, improving colour differentiation between similar groups, and highlighting the key biological findings more clearly would improve accessibility. The heatmap in panel D is particularly difficult to read due to the high density of genes and clusters
- The figure is very crowded and not laid out very well so it is difficult to tell where figure 1B ends and 1C begins making the results more difficult to interpret. Suggest better spreading out of data so its more easily interpreted
  • Figure 1B the data exceeds the axis substantially and one of the graphs has no axis labels or titles at all so its very hard to understand what the data means out with the colour scheme
  • Figure 1D y-axis has so much on it and is extremely small making it difficult to read and interpret. Suggest presenting this in a clearer format for readers to interpret.
  • Figure 1E graphs any form of axis labels so results can’t be clearly interpreted by looking at the data without the rest of the paper/figure legend | |Lots of visual clutter and low readability, colour palette is also overdone without considering the basic colour blind standards. Panel D has very small text, low readability and panel E and B lack clarity in legend. | |Heatmap is very dense and small texts which reduce readability | |Panel C could have more differentiable colours | |Use fewer, more distinguishable colours and a colour-blind-safe palette. Enlarge labels in panels C and D, especially cluster names and gene names. Add a clear colour-scale legend to the heatmap and feature plots. Clarify whether UMAP point density represents individual cells and whether samples were pooled. Make the library/batch information more prominent, since it is important for interpreting single-cell data. | |Splitting the figure could be beneficial to understanding the figure in more detail. | |Reformatted with larger font size for clear presentation of the experimental procedure. | |workflow schematic could do with arrows to show the flow of the process with more space being left between the different parts of the figure to help differentiate them | |The panels could be their own individual figures and more detail could have been given in the legend such as what the arrow is pointing to in A/B? It also isn’t very clear if both UMAPs are a part of B or if the smaller one is part of A, however this is implied in the legend that it is part of B. There is also an issue with how legible the text is because of how much they have tried to cram into the one figure. For the larger UMAP it would have been better if they hadn’t added the labels directly onto the graph since they have a relatively clear legend. | |make gene labels and colour scales clearer and explain the clusters and sample proportions more clearly | |elements feel scattered, not sure where my eyes are supposed to go | |Readability and clarity suffer from the density of the presentation | |More clarification on dimensions/axes in figure b, colour gradient in figure B may be too difficult for people of colour blindness | |No clear focused endpoint of study |

Critique 2.1

Issue

UMAP plots (B, E) are highly manipulable and clustering/placement does not necessarily reflect objective measures.

Solution

Be cautious of over-interpretation of UMAP and other nonlinear dimensionality reduction plots.

Critique 2.2

Issue

Unpleasant clashing (R default) colour choices in (C).

Solution

Use an appropriate colour palette.

Critique 2.3

Issue

The proportion plot in (C) does not give information on absolute number, only proportion/composition.

Solution

A proportional areas plot spanning all clusters would represent both absolute count per group and compositional information.

Critique 2.4

Issue

Heatmap text is too small to read comfortably.

Solution

Present heatmap as a separate figure, or reduce the amount of information in the image.

Critique 2.5

Issue

Heatmap is missing a scale (is purple high and yellow low, or vice versa?)

Solution

Add a scale bar.

Critique 2.6

Issue

The experimental summary in (A) does not indicate order of operations.

Solution

Use arrows to indicate order of steps and/or dataflow.

Critique 2.7

Issue

Text is too small in general to read comfortably.

Solution

Increase font size and/or break up the panels into individual figures.

Critique 2.8

Issue

The figure is crowded and the separation of panels is unclear.

Solution

Use whitespace to guide reader “flow” through the figure and reduce crowding -in particular, cramming (C) under the inset from (B) makes the figure feel very crowded. Alternatively break the panels into multiple figures.

Critique 2.9

Issue

The overall message of the figure is unclear.

Solution

If the intent is just that the macrophages exhibit transcriptional heterogeneity, then (D) is probably sufficient. If other messages are intended, then revise for clarity.

Our Critical Analysis

Post-survey results

Example 3

Figure 3: A C. difficile mutant lacking all three YkuD-type Ldts (\(\Delta\)ldt1-3) exhibits wild-type growth, morphology, and 3-3 cross-linking.

Your Critical Analysis of Example 3

Your Critical Analysis of Example 3

Reasons for the grade
Informative figure legend and a good diagram of cell envelop that conveys what is being investigated. Issues with statistics and obscuring of micrograph
They have a good and clear layout of their data, it is easy to understand and follow. The legend has sufficient information to understand what the figure is about. Good use of white space, good use of colours too which they mention in the legend to help the reader understand what is what and what they are talking about when describing the figure.
clear, informational easy to look at and understand
The first figure is very depictive and I appreciated it for the understanding of the others. However, I dont think they used a good scale on image D, its not clear where the error bars are and where outliers may be. The figure does move logically for the experiment.
Clear presentation of data and clear figure legend. Good use of space and statistical test stated.
clear and concise, looks good
i like it, its clear and gets information across
The figure is well organised & uses clear graphs, diagrams and microscopy images to present the results. The statistical analysis is explained in the legend but still some labels are quite small and could be made bigger for easier reading.
Clear presentation.
good flow
Figure is too crowded and hard to read and legend is too long
Overall informative, statistical analysis included clear individual panels however doesn’t flow great, lots of description on panel A, maybe would be better to represent in figure instead.
The panels are arranged awkwardly, with A and B on the left, C on the right, and D and E squeezed into the middle. There isn’t a clear reading order, each panel is however clear and understandable. Lots of description on panel A maybe too much? Stat analysis included even tho not significant which is good.
Figure legend is too wordy for figure 3a and 3c, a lot of it should be through labelling on tyhe diagram or described in results/discussion. for 3b, legend doesnt fully desribe what is being shown.
clear and easy to interpret, consistent fonts used. significance and tests used to calculate significance are named
they are well presented, easy to understand and nice format.
The figure presents a clear and coherent narrative by combining a conceptual schematic, growth data, microscopy images, morphological quantification, and cell-wall cross-linking measurements. The visualisations are appropriately chosen, easy to interpret, and effectively support the central conclusion that deletion of all three YkuD-type LDTs does not significantly alter growth, morphology, or 3-3 cross-linking.
Good practice by plotting individual data points as dots against summary bars, with a very detailed legend. Great flow of data, excellent scales and well chosen statistical tests. Great colour palette and whitespace management.
Data was lucid. Performed statistical test was mentioned. Significant difference between variants were shown.
Well organised and supportive of study. Different statistical tests might affect consistency and comparison
All the experiments agree. The mutant grows, looks and cross-links like the normal strain.
The figure presents the experimental design, growth data, microscopy, cell length, and peptidoglycan cross-linking results in a logical sequence. The graphs are generally clear, but the figure is crowded and some statistical and replicate information is difficult to assess.
Figure legend is detailed enough to understand the figure. Panels are simplified and clear.
Clear layout, with some minor details overlooked.
The pictures are basic, and it may need look through the whole article.
very clear to follow and figure legend is very clear on what the figure depicts
I can’t find any issues with how the data is presented but in the legend, panels A and C are described in a lot more detail than figure B.
Difficult to understand, graph doesn’t start at 0
the figure is well organised with appropriate graphs and clear experimental details but small sample sizes limit confidence in the results
easily understood, good stylistic choice, didn’t have to read the legend to understand many aspects
Clear and logically organised
Clear, colour blind friendly, good stats
- comprehensive diagram, figure legend has detailed information about experiment
- graphs are clear and understandable with good labelling
missing wavelength and length
Data is very clear, illustrations and microscopy aid understanding for those less familiar with microbiology, growth curves appropriate for analysis

Your Critical Analysis of Example 3

Suggestions for improvement
Use better colour scheme, move labels off image
The figures aren’t in order, it should go A, B, C… but they have done figure 1A and then figure 1C instead of 1B. They have not included a lot of statistical analysis and some more description in certain graphs could help, as some haven’t got much to go on.
I would make the error bars on D clearer. replicates are also shown on D but not E.
B also isnt too clear as they overlap
no
The figure could be improved by increasing the font size of the graph labels and adding individual data points to the bar charts to show variation between replicates. The microscopy images could also be made larger for better visibility.
Bad lay out, I followed it A, C, B, D, E
Bad lay out more than anything
figure legend needs to be revised to be consice but while keeping the necessary information in. some of the figure legend can be brough up as labelling in the figure itself or discussed
The figure is already highly effective, but the growth curve could be improved by displaying individual biological replicate data rather than only means and error bars. Statistical details (exact p-values rather than “ns”) and increased font sizes for some labels would further enhance transparency and readability.
Panel C might have issues with distinguishing between bar colouring, but this is a minor issue.
Few details were missing e.g intensity unit/value of fluorescence heading covering the data in panel c.
The authors say “no difference” because the tests weren’t significant. With only 3–4 repeats, that doesn’t prove the strains are the same.
Show individual data points in panel E, not only bars and error bars.

State the exact number of biological replicates directly on each graph. Explain the error-bar meaning consistently across panels. Consider reducing the size of the schematic in panel A to give more space to the quantitative plots. Use clearer labels for the microscopy scale bars and improve the readability of small text. | |Font size of the numbers in panel B are slightly too small to read. | |Add details. | |C being on the other side of the figure from A and B with E and D in between is slightly confusing but is not too hard to follow | |Potentially more detail for panel B in the legend. | |show individual data points more clearly, report exact p-values and increase the number of biological replicates | |panel layout not intuitive | |Small text size makes it hard to read | |Need to have scale bar for C | |Dot plot for biological replicates for more information |

Critique 3.1

Issue

Dynamite plot: the lower extent of these error bars is not visible.

Solution

Use boxplots or 1D scatterplots

Critique 3.2

Issue

No complement of the triple mutant strain - missing data for an essential control?

Solution

Ensure that all controls are presented so that the experimental result can be interpreted properly.

Critique 3.3

Issue

Label obscures part of the image.

Solution

Relocate the label so data is not obscured.

Critique 3.4

Issue

Fluorescence wavelength not specified.

Solution

Include sufficient information that the reader does not need to refer to the main text. Overall a figure legend should provide enough detail for the figure to stand alone, but should not describe results/significance.

Critique 3.5

Issue

Colour schemes/palettes are inconsistent within panel A, and between panels B, D, and E.

Solution

Be consistent with the visual messaging of colour (hue, saturation, and luminance).

Critique 3.6

Issue

Excessive length of figure legend for panel A.

Solution

Break out panel A into its own figure.

Our Critical Analysis

Post-survey results

Example 4

Figure 4: Functional characterization and overall structure of Rv1217c–1218c.

Your Critical Analysis of Example 4

Your Critical Analysis of Example 4

Reasons for the grade
Bad Western blot, concise figure.
Good layout with figures that look visually appealing, colours used appropriately, good description of the data, indicating what they are describing and has appropriately labelled their figures
clear. colourful but not too much. correctly labelled. easy to follow. legend is clear
They include both vector and WT controls
Figure C is very clear representing different point of views for the models. Using the same colour scheme throughout making it easy to follow
Clear standard of communication and easy to read. It is insightful and labelled in depth.
clear a and b good, c a bit big
i like A and B and D but C is too big and are harder to read.
The figure is well organised and uses clear colours, experimental results and 3D protein structure to present the findings. Some labels are quite small and the structural diagrams can be difficult to understand without referring to the legend.
Visually appealing and clear display of data.
good link to 3D protein structure
Not sure for this one
Are C and D connected to A and B or would it be better to have them in two different figures. Overall it feels a bit random, there is a chemical structure in panel A but unclear what this is or if its necessary, no statistical analysis.
Might be too much detail in the legend almost discussing results? figures individually are good, story/flow is hard to follow. overall feels a bit random. no stat testing in B. Don’t think the figures are all needed? cant understand the overall point clearly
clear decriptions of digrams and diagrams are well made. Legend is slightly difficult to understand at first
X axis of panel B is missing, no title on the panels either
Looks all good, easy to understand the data overall
The figure integrates functional assays, protein expression data, ATPase activity measurements, high-resolution structural information, and topology diagrams, providing multiple complementary lines of evidence. However, the figure is visually crowded, contains several complex panels, and requires substantial specialist knowledge to interpret, reducing accessibility and clarity.
Impressive multi modal integration, very visually appealing, and makes good use of various types of data presentation.
Easy to navigate. Positive and negative controls were performed.
Organised and clear, supportive of study. but quite dense to read
The mutant control is convincing. The E161Q mutant has almost no ATPase activity, and the bacteria lose their rifampicin resistance. This links the protein’s ATP activity to resistance.
The figure combines functional assays, ATPase activity, structural models, and a topology diagram in a logical order. However, the spot assay is mainly qualitative, while the structural panels contain substantial detail that competes with the quantitative evidence.
Detailed figure legend. Fonts are clear.
Some graphics are meaningless, and the color combinations are not well coordinated.
This set of pictures looks very advanced.
very clear layout with figure legend doing very good job of describing the figure. figures used are very clear and easy to understand
I think that the data is very clear and the legend describes the data well but there are a couple of thing I’d say are missing such as statistical analysis of panels A and B if panel A had some absorbance values that show the colour change.
Good labels in A/B. Could potentially use more labels in C/D
the figure combines drug resistance experiments, ATPase activity and structural images but the different data types make it complex to follow
i liked the protein renders, but i have no idea what assay im looking at in panel a, the chemical structure is too small, please show me your entire western blot not just your desired snippet (how do i know youre not hiding something!!!), where is your statistical analysis?
Clearly labelled and follows a logical order
Good use of 3d modelling, dye colour was not explained in figure A in figure legend
confusing layout, hard to understand, bad flow, not sure what the diagram is for
tooooo many colors
Clear mechanistic analysis, evidence of resistance of WT in plates

Your Critical Analysis of Example 4

Suggestions for improvement
dont crop western blot
They have no statistical testing, which figure 4b should have. They could have used Krustal-Wallis or something else. No p-values or significance in this graph either. Not in order, A, B, C… Needs more description and narrative to their legend to help us understand their figure.
no statistical tests
Figure B doesn’t represent statistics, what is the P values, comparison between groups. I also feel that WT should be the first bar
The blots which have been cropped and placed at the bottom feel lost in the graph and it does feel a bit cluttered
I think panel A should be it’s own figure and no need for molecular structure in panel A as it was not explained in figure legend.
no
The figure could be improved by making the labels larger and explaining the colours used in the protein structures more clearly. Adding individual data points to the bar chart would also be helpful to show the variation between experiments.
Unsure if statistical analysis was/needs to be performed for figure B
maybe split the figure into A and B and C and D as struggling to see the connection.
do C and D need to be in this figure could they be separate? maybe dont include the random structure at the top of A especially when its unmentioned in the legend. space things out better
maybe label 4c as front and side view so its completely clear as to what it is showing
The figure would benefit from a clearer visual hierarchy and increased font sizes throughout. Simplifying the structural panels, reducing the number of elements shown simultaneously, improving colour consistency between panels, and adding summary annotations highlighting the key biological findings would make the figure more accessible to a broader audience.
Panel B needs p values or other statistical indicators (asterisks), Panel A can also be slightly confusing due to the location of labels on axis’.
Statistical difference was not mentioned in panel B. Missing immunoblotting data.
The evidence is thin. Only two repeats, no statistics, and a by-eye colour assay make the results less reliable.
Show individual data points and exact p-values in panel B.

State the number and type of replicates and define the error bars. Reduce the amount of structural detail or enlarge key labels. Use consistent colour coding for WT and E161Q across the functional panels. | |Panel A is slightly difficult to interpret with the top, middle and bottom split in the legend. | |Remove meaningless graphics and recombine the colors. | |For panels A and B it would have maybe been more informative if they had some statistical data and if panel A had some absorbance values that show the colour change. I’m also not entirely sure that including the structure of rifamicin was necessary but since they did include it, it could have been better placed. | |make labels and colour keys clearer, improve panel spacing and increase biological replicates beyond two experiments | |dont interpret your data in the legend, make things big enough to see clearly, better descriptions for assays, show me your entire western blot, do stats analysis | |Potentially quite difficult to understand at first glance | |More stats for figure B , Titles for Ribbon presentation | |Low biological replicate number, not robust |

Critique 4.1

Issue

The rifampicin structure is purely decorative.

Solution

Remove unnecessary elements and avoid needless distractions in figures.

Critique 4.2

Issue

Dynamite plot: the lower extent of these error bars is not visible.

Solution

Use boxplots or 1D scatterplots

Critique 4.3

Issue

Colour scheme in (B) doesn’t seem purposeful and doesn’t add anything to the figure.

Solution

Use colour consistently to link or distinguish elements/groups/data, rather than for decoration.

Critique 4.4

Issue

The meaning of the grey regions in (C) and (D) is unclear.

Solution

The implied membrane in (C) and (D) could be labelled as such in the figure. By convention in microbiology, we would assume that the periplasm/extracellular space is “up” and the cytoplasm is “down” in (C) and (D) - but this should really be labelled to avoid any potential confusion.

Critique 4.5

Issue

Colours in (A) difficult to distinguish, especially with the red boxes which seem to skew blue closer to purple.

Solution

Instead of well images, a heatmap with clearer colour distinction could be presented.

Critique 4.6

Issue

Showing two cut-out bands is not an appropriate way to show Western blot data.

Solution

Present the complete blot.

Critique 4.7

Issue

Text in (D) is too small to read easily.

Solution

Break out panel into a separate figure or increase font size.

Our Critical Analysis

Post-survey results

3. Summing Up

General Comments - Data Presentation Choices

Issue

Authors do not always choose the best or most appropriate way to present their data (e.g., dynamite plots)

Solution

When making data visualisation choices, consider how you can best present your data transparently to the reader so that they can evaluate your work (e.g., show the raw data).

Be aware of conventions in the field and discuss with colleagues to come to a consensus of the best and most transparent way to present your data.

General Comments - Colour Choices

Issue

Authors do not always choose the best or most appropriate colours when designing data visualisations.

Solution

When choosing colours, try to:

  1. Be consistent (always use the same colour to represent the same group or feature)

  2. Be accessible (be aware of the different types of colourblindness and design appropriately)

  3. Be aesthetically pleasing (choose colours that work well together, or choose well-designed colour palettes)

General Comments - Readability

Issue

Authors do not always make figures large enough or easy to read.

Solution

When designing figures, make sure that they are appropriately sized and accessible (font large enough to read easily at 100% size).

Include enough space between panels of a figure that allows the figures to “breathe” - the eye should flow smoothly from one element of the figure to the next in a natural way.

Try printing out a copy of the figure and look at it from arm’s length to see how it feels in terms of whitespace and use of “real estate” - then make appropriate edits to improve the figure.

General Comments - Message

Issue

Authors sometimes include too much data in a figure, or make a figure overwhelming in other ways.

Solution

When sitting down to make a figure, be sure to define a clear message in the first instance. Present the data that are necessary to convey that message. Remove anything extraneous. (Split into multiple figures if necessary.)

Some Very Insightful Comments From You

  • “The data is presented in a manner that would likely be inaccessible for people without prior experience. A move toward a more palatable/digestible format will facilitate better science communication in the future.”

  • “I think that it is also crucially important to learn how to present data well and responsibly…”

Further Reading