"colors" setting in "add_track"

[grimwoo]

Thank you for the development of Plot1Cell. This issue is related to issue #6.

Here, I set the collor for plot_circlize and add_track. The plot_circlize works perfectly. But the add_track only use the ordered colors for each clusters, rather than use the correct color for each subsets clusters.

The code is as the following : ` Order_Celltype_Main <- c( "EC","VSMC", "FC","CPC","PreHTC","RegC", "M1 macrophage" ) color_Celltype_Main <- c( "#F8766D","#C49A00", "#53B400","#00C094","#00B6EB","#A58AFF", "#FB61D7" ) names(color_Celltype_Main) <- Order_Celltype_Main Seurat.object$Celltype_Main <- factor( x = Seurat.object$Celltype_Main, levels = Order_Celltype_Main )

Order_Celltype_Subset <- c( "EC (SELE)", "VSMC (IL6)","VSMC (RGS5)",

"FC (AQP3)","FC (CFH)", "FC (ECRG4)","FC (FOS)", "FC (HSPB1)","FC (POSTN)", "FC (PRG4)","FC (THBS4)", "FC (LOC119877775)","FC (MAGI2)", "FC (MMP3)","FC (MT1E)", "FC (RBP4)","FC (S100A12)",

"CPC (STMN1)", "PreHTC (MMP3)", "RegC (PTGS2)",

"M1 macrophage (CCL23)","M1 macrophage" ) color_Celltype_Subset <- c( "#F8766D", "#e0b311", "#b4900e",

"#9DB400", "#90B405", "#84B40B", "#78B411", "#6CB417", "#60B41D", "#54B423", "#48B428", "#3CB42E", "#30B434", "#24B43A", "#18B440", "#0CB446", "#00B44C",

"#00C094", "#00B6EB", "#A58AFF",

"#dd40b8", "#df74c6" ) names(color_Celltype_Subset) <- Order_Celltype_Subset Seurat.object$Celltype_Subset <- factor( x = Seurat.object$Celltype_Subset, levels = Order_Celltype_Subset )

Plot1Cell.object <- prepare_circlize_data(Seurat.object, scale = 0.8 )

Plot1Cell.object$Celltype_Main <- factor( x = Plot1Cell.object$Celltype_Main, levels = Order_Celltype_Main ) Plot1Cell.object$Celltype_Subset <- factor( x = Plot1Cell.object$Celltype_Subset, levels = Order_Celltype_Subset ) Plot1Cell.object$Sample <- factor( x = Plot1Cell.object$Sample, levels = Order_Sample )

plot_circlize( Plot1Cell.object, do.label = T, contour.levels = c(0.1, 0.5, 0.9), pt.size = 0.25, col.use = color_Celltype_Main , bg.color = 'white', kde2d.n = 1000, repel = T, label.cex = 0.7)

add_track( Plot1Cell.object, group = "Celltype_Subset", colors = color_Celltype_Subset, track_num = 2) `

[grimwoo]

[grimwoo]

The left two figures show the correct color I set.

The right figure shows the correct color of "Celltype_Main" by plot_circlize and the wrong color of "Celltype_Subset" by add_track.

Could you please help me?

[grimwoo]

@HaojiaWu

[HaojiaWu]

@grimwoo The issue should have been fixed. Please reinstall the package:

devtools::install_github("HaojiaWu/plot1cell")

Then, use these lines:

color_Celltype_Subset <- c(
"#F8766D",
"#e0b311", "#b4900e",
"#9DB400", "#90B405", "#84B40B", "#78B411",
"#6CB417", "#60B41D", "#54B423", "#48B428", "#3CB42E",
"#30B434", "#24B43A", "#18B440", "#0CB446", "#00B44C",
"#00C094",
"#00B6EB",
"#A58AFF",
"#dd40b8", "#df74c6"
)
add_track(
Plot1Cell.object,
group = "Celltype_Subset",
colors = color_Celltype_Subset,
track_num = 2)

Let me know if it doesn't work.

[grimwoo]

@HaojiaWu Thank you for your quick reply. However, after your guidance, I still cannot get the correct color of the sub-cell types.

My package version is 0.0.0.9000 after reinstall.

Or could you help me with the annotation of the plot ? I can accept the default colors, if the plot shown me which color reference to which sub-celltype.