klebgenomics/kleborate-viz

Visualisation application for Klebsiella genotypes generated by Kleborate.

kleborate-viz's Issues

Add group number selector to Genotypes by STs tab

Started filling in using Genptypes by ST tab as a guide. Slider shows but only seems to allow max 1 group. Not sure why this isn't working.

add K and O locus plot tab

fix the summary table

remove V1/V2 and add any other useful rows

Species summary - order the legend so that KpSC is always shown at the top

Think this should be possible with similar logic as used to specify consistent colours for KpSC?

fix colours on stacked species bars

make the Kp complex species have more distinguishable colours

on summary page, select values from bar plot

e.g. could we select a bar (say Klebs pneumo, res score=3) and use this to populate the plots, so that the virulence distribution plot is then just showing the vir scores of these strains? is this useful? or is it best got from the heatmaps tab... perhaps most useful if this carries over to the ST distribution plot, as we are then seeing ST distribution of subpopulation with res or vir score characteristics selected on summary page

MIC plots need y-axis to be on log scale

Temporal trends - add year selector bar

Can we add a selector bar that allows users to select the range of years to display in the plots? Perhaps at the top of the page so that it is easy to spot?

Web not open

The website is not open now. Is this site under maintenance for any reasons? Thank your work about Kleborate and Kleborate-viz. These analysis tools are very useful. Thank you!

make the species toggles reactive

Work on convergence ST/heatmap tab

To do:

• add res/vir scores to rows (strains) using RowSideColors or row_side_colors
• add gene frequency to columns (genes) using col_side_colors
• make sure can download data & plots with plotly controls; or add new buttons
• consider adding ICEKp types? or perhaps just use this selection to populate another heatmap in another tab, to show full vir subtype and full resistance gene info (here we only have classes)

add download PDF to all plots

Add group and colour by selectors to sample trends tab

Started filling in the code - the selectors are in place and showing the correct options but can't seem to get the reactivity to work and plot to show. Currently commented out new code so that plot is showing with previous working code.

Kleborate-viz not uploading the file

Hi team Kleborate-viz

Im trying to upload my kleborate data into kleborate-viz, but as soon as the file uploads, i get an error stating disconnected from server. Kindly suggest what could be the reason for the error, I have tried to switch the systems but the problem persists.
Hopefully you can help me out.
Thanks in advance, anticipating for a quick response

change default species selection to have 'Others' switched to FALSE

Genotypes by STs - make barplot legend title match the dropdown text

Currently the legend title is the raw column name, but the dropdown list shows a cleaner version - can we replicate that to the legend?

add legends to 'temporal trends' plots

Enable PathogenWatch data upload - high priority

The Kleborate table that can be downloaded from Pathogen Watch should include all the columns we need (num_res_genes and num_res_classes currently missing but we've asked them to update and they've agreed to do so) BUT its in csv rather than tab delim format and the genome id column is called 'Genome Name' instead of 'strain'.

Can we enable tabdelim OR csv upload via the same button?

Thinking we can add a check after upload for 'strain' in colnames() and if not present we can do mutate(strain = Genome Name) so that the fix is propagated through all code. Is this possible?

Other option could be to add a second upload button to specifically handle PW output instead of direct Kleborate output - then we could just read in csv and immediately update the Genome Name column. In that case, either the standard Kleborate output or the PW Kleborate output would be required.

MICs by genotypes tab - add dropdown box to select AMR genotype for X-axis

Dropdown box to select from three columns ("carbapenemase_omp_combination", "ESBL_omp_combination", "Bla_acquired_omp_combination") - I've already added the code that creates these columns.

One tricky part is that we need to specify the x-axis order because alphabetical isn't ideal, and the order changes based on the genotype that is selected.

For carbapenemases: limits=c("- wt", "- mut", "IMP wt", "IMP mut", "KPC wt", "KPC mut", "NDM wt", "NDM mut", "OXA wt", "OXA mut", "VIM wt", "VIM mut", "other wt", "other mut", "multiple wt", "multiple mut")

For ESBLs: limits=c("- wt", "- mut", "CTX-M-14 wt", "CTX-M-14 mut", " CTX-M-15 wt", "CTX-M-15 mut", "CTX-M-65 wt", "CTX-M-65 mut", "SHV wt", "SHV mut", "TEM wt", "TEM mut", "other wt", "other mut", "multiple wt", "multiple mut")

For Bla_acquired: limits=c("- wt", "- mut", "DHA wt", "DHA mut", " LAP wt", "LAP mut", "OXA wt", "OXA mut", "TEM wt", "TEM mut", "other wt", "other mut", "multiple wt", "multiple mut")

Add plots showing freq of individual K/O loci

for all samples currently selected, or stratified by ST
could be barplots or heatmaps?

Big fix - heatmap on Convergence by STs tab no longer working on ST selection

Looking at https://kleborate.erc.monash.edu/ - when I try to select an ST I get an error in the heatmap both selecting from the plot and using the new ST box

add button to download ST summary data on relevant tabs

e.g. on ST distribution tab, would be useful to download the tabulation of ST vs current variable being displayed

Cumulative K/O locus tab - add dropdown box for selecting metadata variable to group by

Need to check for column names in the metadata file to populate the drop down list and edit the calls to prop.table in cumulative_ko_locus.R to use the selected variable instead of 'Region' - rest of code should then work.

Ideally also edit colours to a nicer palette - need to figure out how to do this when don't know the total number of groups - see also the 'Trends by sample' tab.

check for all data columns and give sensible errors

e.g if species columns K or O locus cols or resistance gene cols are absent - give a message to rerun Kleborate using --all option.

enter specific ST to show heatmaps

Currently the heatmaps of AMR/vir (on convergence tab) and K/O are populated by an ST chosen by clicking on the interactive scatter plot on the same page. But if a user wanted to see the heatmap for a given ST they would have to find it in the scatter plot which is a pain. Would be good to also allow users to simply type in a ST to populate the heatmap with (would need appropriate checks to see if it exists etc).

make res/vir heatmap clickable

i.e. use the heatmap to select convergence zones to show detail of strains in that zone

• the result could be a ST barplot next to the heatmap (because it doesn't need much width), and a heatmap of specific vir/res genotypes below (annotated with ST ideally)
• could optionally switch the primary res vs vir heatmap axes to be number of res/vir classes rather than scores; or total number of res genes

Add colour options for genotypes by ST and genotypes by metadata

Add options to colour by:
*ST category e.g. MDR, hv, other - will need to specify a list of MDR and hv STs in global
*ybt lineage
*iuc lineage
*iro lineage
*rmpADC lineage
*rmp truncations
Kelly to provide code to process data and colour palettes to match Maggie's figures.

Bug fix - colours in heatmap on Convergence by ST tab

When there are no resistance determinants in a set of genomes the virulence columns get coloured red, when they should be blue - e.g. see KASPAH data set- ST86.

silence plot warnings

e.g st distribution plot warning about removing rows with non-finite values

Vir vs res heatmap on 'Genotypes by ST' tab

I like this as a heatmap, but as a data selector on this page it serves a very limited purpose since it seems to only allow one (x,y) point to be selected. It would be more useful if you could select a range. But actually this can be done easily with the slider in the left-hand controller.
It might be more useful on the 'Summary by species' tab... i.e. turn this into 'Summary' tab which would show virulence & res score barplots, and the vir vs res heatmap.
Alternatively, if it could be embedded in the left-hand controller as the selector for vir/res score range rather than the sliders that would be really cool.

MIC data upload refresh

MIC table upload doesn't refresh in the control bar when user uploads new kleborate output (but metadata does).
When MIC tables is uploaded the MIC plot only appears if a metadata table is also uploaded. No metadata is used in the MIC plot so I think these should be independent.

K/O diversity - show rownames for K loci in heatmap if <= 20 rows? - low priority

Turn off K/O locus plots if K/O columns are not present in the output

Remembered that it is possible to run Kleborate without Kaptive and so I think it would be useful to eloquently handle the case when these columns are missing.
It is also possible to run Kleborate with resistance screening turned off but these data are central to the majority of the plots so I think it is fair to say that Kleborate-viz is going to expect resistance typing to be turned on (?) Also most people are interested in resistance so likely have it turned on anyway.