Samuel Granjeaud

Integrating HSNE?

2

Hi, Thanks for your invaluable work proposing umap in a native R package. Thanks also for the smallvis package. As you already integrated largeVis and proposed tumap, I am wondering...

Any plan for API like RcppHSNW or RANN?

7

Thanks for your package. I would like a more "classical" interface to this library, which would simplify its use, at least mine. Any plan? Best.

Error: NMF::nmf - Input matrix x contains at least one null or NA-filled row.

2

Seems to occur when all the values in one row are zero. The message should reflect this if I am correct.

Hi, Thanks for this package and comparing the various approaches to solve conflicts. Could you update the comparison with the [box](https://github.com/klmr/box) package as the [modules](https://github.com/klmr/modules) package is deprecated? box sounds...

plotDiffHeatmap : ambiguity when multiple clusterings could match

2

IIUC, when multiple columns of `cluster_codes` could match the levels of `cluster_id`, the first one is selected silently. https://github.com/HelenaLC/CATALYST/blob/f3e294ed9a4d3f300feb994bb381df6a6b2c8309/R/plotDiffHeatmap.R#L140-L151 IMO, if `sum(same) > 1` a warning must be raised show...

plotDiffHeatmap: avoid failure when only one cluster remains

4

IIUC, when there is only one cluster left, `as.matrix()` results in a one column matrix instead of one row matrix. https://github.com/HelenaLC/CATALYST/blob/f3e294ed9a4d3f300feb994bb381df6a6b2c8309/R/plotDiffHeatmap.R#L243-L250 I propose to transpose y in such a case....

Hi Sofie, Does the gsub mean basename? At https://github.com/saeyslab/CytoNorm/blob/e94732cec4ce26c44d167c530978b2c5b296e55c/R/QuantileNorm.R#L494-L495 I think it you would interesting to store the untransformed along with the transformed channels. This redundant with the quantile plot...

Hi Sofie, I think there is something missing in the sentence > normParams takes "nQ", the number of quantiles. Additionally, quantile_values The goal can be "mean", one of the batch...

Hi, There is an issue in https://github.com/ImmuneDynamics/Spectre/issues/169 that related to the following line https://github.com/saeyslab/FlowSOM/blob/ec21465eb612a1a74cbbb5bd2cb21953f540a8af/R/0_FlowSOM.R#L269 I think the & should be replaced by &&. Maybe the rest of the code should...

Could you build a specific function for plotting of outliers?

2

Hi, I think it would be clearer and useful to thave a plot function outside of the TestOutliers function. From my experience, it is better to separate computation and graphics....