Attach a X-axis/bar of Pseudo-time value/cell cluster color bar on the top of the plotTrajectoryHeatmap

[willey2020]

Hello! Thanks again for this great package!

Describe the problem that your feature request would address.

The plotTrajectoryHeatmap function is very cool.
The y axis of the current plots(TF motif,Gene score, RNA) is very clear. However, it is better to get an accurate sense about which time point, a feature(motif,gene,RNA) is showing up/down, maybe through a more detailed x-axis or color bar, for example, the pseudo-time x axis or the pesudotime/cell cluster color bars, on the top of the trajectory heatmap.

Describe the solution you'd like
Is there any way to attach a x-axis that shows pesudotime value according to the heatmap,like below or on the top of the heatmap? Then, we can get a sense of exactly when a TF/RNA/gene score is upregulated/downregulated.

Describe alternatives you've considered
If there is another way, that shows the matched color the pesudotime value (dark blue, purple to yellow, showed in manual 16.1.1) in a horizontal color bar plot, and matching the trajectory heatmap x-axis, then it will be much more clear.

Or if there is a way to shows the cell cluster color bar together matching the x-axis, it will be great!

For these two alternative solutions, I attached two reference plots, examples from single-cell RNA-seq study. Just for examples only. For the second example, their cell type/stage colors showing on the top of the heatmap are a similar analogy to cell cluster color.

Additional context
After searching in the issues, not sure if a similar feature request was posted before.
Thank you so much and again this is a great and amazing package!

[rcorces]

I dont think this is currently possible but seems reasonable. Feature requests have piled up so I wouldnt expect this to be addressed soon though.

[willey2020]

Thank you!! Totally understand! Thanks again for this great package!

[hjc0818]

Hi there, I am using the package and found that this feature is important. While I found some code in their Nature Genetic paper can do this. Please see below

https://github.com/winstonbecker/scCRC_continuum/blob/main/scATAC_stromal.R

line 1028 - 1039

trajGIM <- getTrajectory(ArchRProj = proj_stromal, name = "control_caf_trajectory", useMatrix = "GeneIntegrationMatrix", log2Norm = TRUE) p3 <- plotTrajectoryHeatmap(trajGIM, pal = paletteContinuous(set = "blueYellow"), labelTop = 20, varCutOff = 0.6) plotPDF(p3, name = "Plot-control_caf_trajectory-GIM-Heatmap.pdf", ArchRProj = proj_stromal, addDOC = FALSE, width = 6, height = 10) test <- getCellColData(proj_stromal)[!is.na(getCellColData(proj_stromal)$control_caf_trajectory),c("CellType", "control_caf_trajectory")] as.matrix(test[order(test$control_caf_trajectory),"CellType"]) new_df <- data.frame(cbind(test[order(test$control_caf_trajectory),"CellType"], c(1:3043), rep(1,3043))) new_df$X2 <- as.numeric(as.character(new_df$X2)) p <- ggplot(new_df, aes(X2, X3)) + geom_tile(aes(fill = X1)) + scale_fill_manual(values= c("#272E6A", "#0C727C", "#6E4B9E"))+theme_ArchR()+theme(axis.text.x = element_text(angle = 90)) plotPDF(p, name = paste0("caf_control_trajectory_hm.pdf"), width = 5, height = 5, ArchRProj = proj_stromal, addDOC = FALSE)

Hope it helps, and I hope someone can incorporate this code into the plotTrajectoryHeatmap function, since right now its just giving out a heatmap without any label on top. Will be very frustrating for non-hardcore users.

Sincerely

Han.

[rcorces]

@hjc0818 - thanks for the reminder. I had half-way coded this and lost track of it.
I've incorporated this into the dev_trajectoryHeatmap branch. You can install that branch like so:

devtools::install_github("GreenleafLab/ArchR", ref="dev_trajectoryHeatmap", repos = BiocManager::repositories())
#to unload a package and reload
detach("package:ArchR", unload=TRUE)
library(ArchR)

After installing, you will need to re-run getTrajectory() paying special attention to the new trajectoryLabel parameter:

ArchR/R/Trajectory.R

Lines 290 to 292 in 586c8a9

	#' @param trajectoryLabel The name of a column in `cellColData` to be used for labeling the quantile bins of the trajectory.
	#' This is used in `plotTrajectoryHeatmap()` when you want to create a color label for the columns across the top
	#' of the heatmap. Typically, this should be the same column used in `groupBy` in the `addTrajectory()` function.

Then you will run plotTrajectoryHeatmap() and include the new colorColumns and columnPal parameters:

ArchR/R/Trajectory.R

Lines 470 to 475 in 586c8a9

	#' @param colorColumns A boolean value that indicates whether a color bar should be added to label the columns. The color for each column
	#' will represent the most common label observed in the corresponding trajectory quantile as the heatmap is divided into quantile bins
	#' and thus does not display information for each cell. `colorColumns` can only be set to `TRUE` if the `trajectoryLabel` parameter was used
	#' in `getTrajectory()`.
	#' @param columnPal A discrete palette (see `paletteDiscrete()`) that maps the different labels of the trajectory to a unique color. This
	#' parameter is ignored unless `colorColumns = TRUE`. All labels shown in `unique(colData(seTrajectory)$label)` must be represented.

Please let me know if this works for you. If so, I will merge these changes into dev for future incorporation into release_1.0.3

Example below:

trajectory <- c("Progenitor", "GMP", "Mono")

projHeme5 <- addTrajectory(
  ArchRProj = projHeme5, 
  name = "MyeloidU", 
  groupBy = "Clusters2",
  trajectory = trajectory, 
  embedding = "UMAP", 
  force = TRUE
)

trajMM  <- getTrajectory(ArchRProj = projHeme5, name = "MyeloidU", useMatrix = "MotifMatrix", log2Norm = FALSE, trajectoryLabel = "Clusters2")

p1 <- plotTrajectoryHeatmap(trajMM, pal = paletteContinuous(set = "solarExtra"), colorColumns = TRUE, columnPal = paletteDiscrete(values = unique(colData(trajMM)$label)))

plotPDF(p1, name = "Plot-MyeloidU-Traj-Heatmaps.pdf", ArchRProj = projHeme5, addDOC = FALSE, width = 6, height = 8)

[rcorces]

@hjc0818 - could you test this out please?

[taminastelzer]

Hi, first of all thanks for the great tool. I really enjoy working with ArchR. I am currently doing a lot of Pseudotime Trajectory analysis. For this, I would like to add a X-axis/bar of cell cluster on the top of the plotTrajectoryHeatmap. While searching for this possibility, I came across this issue. However, unfortunately I am not able to install the dev_trajectoryHeatmap branch. I receive following Error message:

Downloading GitHub repo GreenleafLab/ArchR@dev_trajectoryHeatmap Error in utils::download.file(url, path, method = method, quiet = quiet, : cannot open URL 'https://api.github.com/repos/GreenleafLab/ArchR/tarball/dev_trajectoryHeatmap'

Is this branch not present anymore? I would highly appreciate your help!

Thanks a lot!

[rcorces]

this was merged into the dev branch.