Thresholds for plotted Z-scores in Dotplot2

[kzb193]

Hello,

Is it possible to control the plotted Z-score thresholds in Dotplot2() ? I am looking for something similar to col.min and col.max in DotPlot().

[kzb193]

Hello,

Please let me know if you have any updates on this. Thanks!

[huayc09]

Hi! Thanks for the suggestion. I've just added col.min and col.max parameters to DotPlot2(). You can now use them like this:

DotPlot2(seu, features = genes, col.min = -1, col.max = 1)

This will clip z-score values to the specified range, similar to Seurat's DotPlot(). The default is NULL (no limits).

[kzb193]

Thanks a lot!

[kzb193]

Hi,

One quick follow-up.
Is it possible to add the same feature in Heatmap() ?

[kzb193]

I think the new feature is not generating plots as expected. In the following example, the outputs remain same along with some warnings.

library(SeuratExtend)

grouped_features <- list(
"B_cell_markers" = c("MS4A1", "CD79A"),
"T_cell_markers" = c("CD3D", "CD8A", "IL7R"),
"Myeloid_markers" = c("CD14", "FCGR3A", "S100A8")
)
DotPlot2(pbmc, features = grouped_features)
DotPlot2(pbmc, features = grouped_features,col.min=-1,col.max=1)
DotPlot2(pbmc, features = grouped_features,col.min=-0.5,col.max=0.5)

Warning messages:
1: In plot_theme(plot) :
The col.min theme element is not defined in the element hierarchy.
2: In plot_theme(plot) :
The col.max theme element is not defined in the element hierarchy.

[kzb193]

Hi,

Please let me know if you have any updates on this issue.

[kzb193]

Hi,

I hope you are aware of this issue. Looking forward for a solution!
Thanks!

[huayc09]

Hi, I've been really busy lately, so haven't had a chance to address this thread yet. I should be able to push an update this week and resolve a few issues though. Thanks for your continued attention to this and for supporting SeuratExtend!

[kzb193]

Thank you so much! Love SeuratExtend! It is extremely useful.

[huayc09]

Hi,

Thanks for testing! I've verified that the col.min and col.max parameters are functioning correctly.

Based on the warning message you received, it appears the issue was caused by using an outdated version of the package. The warnings indicate that col.min and col.max were being passed to theme(), which only happens when these parameters aren't defined in the function signature (i.e., in the old version).

Please reinstall the package from GitHub:

remotes::install_github("huayc09/SeuratExtend")

After installation, restart your R session and try again. The issue should be resolved.

Additionally, I've implemented the same col.min and col.max parameters for Heatmap() as well. Feel free to test this feature after updating!

You can verify you have the updated version by checking:

args(DotPlot2)

You should see col.min = NULL and col.max = NULL in the parameter list.

[kzb193]

Thank you so much!! Tested Dotplot2. No more issues.