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zhanghao-njmu / SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
https://zhanghao-njmu.github.io/SCP/
GNU General Public License v3.0
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Error in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y #120

Open bio-visualisation opened 1 year ago

bio-visualisation commented 1 year ago

Do you have any idea why I am getting this grid.call error while running DynamicPlot() and DynamicHeatmap() DynamicPlot( srt = cortex, lineages = c("Lineage3", "Lineage7"), group.by = "Hes_Exp", features = c("Nes"), compare_lineages = TRUE, compare_features = FALSE)

[2023-03-23 19:14:25] Start RunDynamicFeatures Workers: 78 Number of candidate features(union): 1 Calculate dynamic features for Lineage3... |==========================================================================================| 100%

[2023-03-23 19:15:06] RunDynamicFeatures done Elapsed time:40.59 secs [2023-03-23 19:15:06] Start RunDynamicFeatures Workers: 78 Number of candidate features(union): 1 Calculate dynamic features for Lineage7... |==========================================================================================| 100%

[2023-03-23 19:15:46] RunDynamicFeatures done Elapsed time:40.35 secs Warning in DynamicPlot(srt = cortex, lineages = c("Lineage3", "Lineage7"), : Values in 'counts' slot is non-integer. Set the libsize to 1. Warning in DynamicPlot(srt = cortex, lineages = c("Lineage3", "Lineage7"), : Values in 'counts' slot is non-integer. Set the libsize to 1. Error in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : polygon edge not found (zero-width or zero-height?)

zhanghao-njmu commented 1 year ago

This error is not related to SCP, it seems to be a font issue. However, I have tried to find several solutions for you.

In general, you can try updating the ggplot2 and related packages and then save the image using ggsave() instead of directly outputting it in the view window to avoid errors.

If this does not work, there are also some discussions and solutions related to this issue in the following links:

https://github.com/tidyverse/ggplot2/issues/2252 https://stackoverflow.com/questions/10581440/error-in-grid-calll-textbounds-as-graphicsannotxlabel-xx-xy-polygon https://stackoverflow.com/questions/71362738/r-error-in-grid-callc-textbounds-as-graphicsannotxlabel-xx-xy-polygo

bio-visualisation commented 1 year ago

I tried updating ggplot2. Then tried using ggsave(). Tried other solutions with theme(text = element_blank()) if it was a font issue. But none of them is making any difference.