-
Notifications
You must be signed in to change notification settings - Fork 25
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
"colors" setting in "add_track" #7
Comments
The left two figures show the correct color I set. The right figure shows the correct color of "Celltype_Main" by Could you please help me? |
@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. |
@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. |
Thank you for the development of Plot1Cell. This issue is related to issue #6.
Here, I set the collor for
plot_circlize
andadd_track
. Theplot_circlize
works perfectly. But theadd_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)
`
The text was updated successfully, but these errors were encountered: