x-axis order using split.by

[misterygirl2]

Hi,

I used split.by="Experiment" function to list the order of the x-axis labels like the first image, but the order of the x-axis keeps appearing as in the image below. How can I fix it?

Thanks!

[zktuong]

Hi @misterygirl2, thank you for alerting me to this.

I've added a fix to this in #17 which I will merge to master once checks are complete.

The way to interact with this once the fix is merged is to change the factor levels of the split.by column in the single-cell data:

library(ktplots)
library(Seurat)
data(kidneyimmune)
data(cpdb_output)

levels(kidneyimmune$Experiment)
#  [1] "PapRCC"  "RCC1"    "RCC2"    "RCC3"    "Teen Tx" "TxK1"    "TxK2"    "TxK3"    "TxK4"    "VHLRCC"  "Wilms1" 
# [12] "Wilms2"  "Wilms3" 

plot_cpdb(cell_type1 = 'B cell', cell_type2 = 'CD4T cell', scdata = kidneyimmune,
    idents = 'celltype', # column name where the cell ids are located in the metadata
    split.by = 'Experiment', # column name where the grouping column is. Optional.
    means = means, pvals = pvals,
    genes = c("XCR1", "CXCL10", "CCL5"))

This is the original, and creates the following plot:

Now, by adjusting the factor levels in the split.by column in the single-cell data:

kidneyimmune$Experiment <- factor(kidneyimmune$Experiment, levels = c("Wilms2", "TxK1",  "RCC2", "RCC3", "TxK4", "VHLRCC", "Wilms1", "PapRCC", "RCC1",  "Teen Tx", "TxK2", "TxK3",  "Wilms3"))

plot_cpdb(cell_type1 = 'B cell', cell_type2 = 'CD4T cell', scdata = kidneyimmune,
    idents = 'celltype', # column name where the cell ids are located in the metadata
    split.by = 'Experiment', # column name where the grouping column is. Optional.
    means = means, pvals = pvals,
    genes = c("XCR1", "CXCL10", "CCL5"))

we get this plot:

I will update this thread again once it's been merged.

[zktuong]

Ok it's now been merged. Please re-install and check that ktplots is now version 1.1.10.

Feel free to let me know if there's any other issues.

Thank you,

Kelvin

[misterygirl2]

It works well! Thanks!!