geom_stats static location

[alexheubeck]

Hi @jacobpwagner,

I had a quick question about using geom_stats. I am trying to plot a boolean NOT gate with ggcyto, and display the stats for that population. I'm using the adjust parameter to change the location of the gate info. However, since it is relative to centroid of the population, the stats box is moving around a lot more than I'd like when the population shifts more than usual. Is there a way to have a static position for the geom_stats info on a plot? I saw that you could add arguments from geom_label, but I couldn't get anything to work.

Here's an example where the 'Non-Treg' population is a boolean NOT gate of the 'Treg' gate:

Thanks,

Alex

[jacobpwagner]

Interesting, I believe this should be what the abs parameter is for at the level of stat_position. However, that is currently not recongized by geom_stats and thus not passed down to stat_position. Let me see if I can fix this quickly.

[jacobpwagner]

After 0cdb186, adding abs=TRUE to geom_stats should set the starting point for adjust to the center of the whole ("absolute") data range as opposed to the subset in the gate. Note that this still doesn't mean the center of the window, as that would probably require adding an extra static arg that triggers a bypass of the centroid logic entirely. That's certainly doable as well so I'll probably leave the issue open to track that. However, exposing abs was an easy addition so I thought it was worth adding it first.

Additionally, @mikejiang , it looks like there was already logic to automatically set abs=TRUE for booleanFilters . For now I just made sure that automatic logic doesn't override explicit abs=TRUE from the user. I'm not sure why it wasn't getting triggered here but it could be a class inheritance issue or something. I'll look into it as time allows.

Examples below:

Setup:

library(flowCore)
library(flowWorkspace)
library(ggcyto)
gs <- load_gs(system.file("extdata", "gs_manual", package = "flowWorkspaceData"))

Position: default -- center of gate

ggcyto(gs[[1]], aes("CD4", "CD8"), subset = "CD3+") +
  geom_hex(bins = 0) +
  geom_gate("CD4") +
  geom_stats()

Position: lower left with respect to center of gate range

ggcyto(gs[[1]], aes("CD4", "CD8"), subset = "CD3+") +
  geom_hex(bins = 0) +
  geom_gate("CD4") +
  geom_stats(adjust = c(0.1, 0.1))

Position: center of full data range

ggcyto(gs[[1]], aes("CD4", "CD8"), subset = "CD3+") +
  geom_hex(bins = 0) +
  geom_gate("CD4") +
  geom_stats(abs = TRUE)

Position: lower left with respect to center of full data range

ggcyto(gs[[1]], aes("CD4", "CD8"), subset = "CD3+") +
  geom_hex(bins = 0) +
  geom_gate("CD4") +
  geom_stats(adjust = c(0.1, 0.1), abs = TRUE)

Note this is still not with respect to the range of the window (just the data):

ggcyto(gs[[1]], aes("CD4", "CD8"), subset = "CD3+") +
  geom_hex(bins = 0) +
  geom_gate("CD4") +
  geom_stats(adjust = c(0.1, 0.1), abs = TRUE) +
  ggcyto_par_set(limits = list(x = c(-10000, 4000), y = c(-1000, 4500)))

[alexheubeck]

Hi @jacobpwagner,

Thanks for that fix. It's working better, as the label moves less, but it still gets moved off of the plot sometimes when the populations shown are atypical. Adding the static argument would be great, but as time allows.

[jacobpwagner]

Hi @alexheubeck. I'll get to work on the static option. Just out of curiosity, could you show a case where the label is getting moved off the plot? I just want to also make sure that that last fix is behaving as expected.

[alexheubeck]

I want the label to sit in the top right, opposite the other label.
These two plots have the correct placement:

These two are cases where it gets moved off:

[jacobpwagner]

Gotcha. And are you using ggcyto_par_set to manually change the limits of the window? I just want to make sure I understand how it's getting pushed off. Also, it looks like the static option will be a simple addition as well.

I'm adding an argument that determines what range to use to determine the starting point for the label. It will allow the 3 options:

• gate range -- abs = FALSE in the old argument -- "gate" (and default) for the new arg
• data range -- abs = TRUE in the old argument -- "data" for the new arg
• whole plot range -- not possible with the old args -- maybe "plot" or "window" for the new arg

As a user, if there's a name for this argument (and the whole plot range option) that makes the most sense, I'd be happy to get your input. Currently, I'm using location, so it would be location="gate", location="data", or location="plot". I thought about window instead of location as well, but thought that might confuse the purpose of the argument which is just to determine the starting location for the label that can then be moved around with adjust.

[alexheubeck]

I am using ggcyto_par_set. This is the line I'm using for that plot:

Treg <- ggcyto(gs[[idx]], aes(x = CD127, y = CD25), subset = "CD4 T Cells",) + geom_hex(binwidth = c(0.015,0.015)) + ggcyto_par_set(limits = list(x = c(1,3.5), y = c(1,4))) + geom_gate('Treg' ,col='black') + geom_stats("Treg", type = c("gate_name", "percent"), adjust=c(0.1,0.95), size=1.5, fill="transparent") + geom_stats('Non-Treg',type = c("gate_name", "percent"), adjust=c(0.95, 1), abs=TRUE, size=1.5, fill="transparent") + axis_x_inverse_trans() + axis_y_inverse_trans() + theme_bw() + mytheme + facet_null() + scale_fill_gradientn(colours = matlab.like2(300), trans = "sqrt")

(Sorry it's a mess)

I think location makes sense. Since I'm using a static range for the plot, my ideal way of doing this would be to provide coordinates on the plot for the center of the label. For example, if the range of both axis is (0,4), I could set the center of the label to (3.5,3.5) so it always stays in that static location. I'm assuming that's what you're doing with the "whole plot range" argument.

[jacobpwagner]

Cool, I'll go with location then. Regarding the specification of the location for adjust, I could also add a "fixed" option to handle your use case. That is, instead of:

ggcyto(...) +
... +
ggcyto_par_set(limits = list(x = c(0,4), y = c(0,4)) +
geom_stats(location = "plot", adjust=c(0.875, 0.875))

you could instead do this:

ggcyto(...) +
... +
ggcyto_par_set(limits = list(x = c(0,4), y = c(0,4)) +
geom_stats(location = "fixed", adjust=c(3.5, 3.5))

Does that sound about right? That seems like a pretty reasonable request and addition.

[alexheubeck]

Yeah that's perfect, thanks!

[jacobpwagner]

Alright, after f0a4d42, this is now possible. Here are some examples using the same setup as before. I include the ggcyto_par_set adjustment of axis limits to demonstrate how they are ignored or used in each case:

Default positioning

 ggcyto(gs[[1]], aes("CD4", "CD8"), subset = "CD3+") +
  geom_hex(bins = 0) +
  geom_gate("CD4") +
  geom_stats() +
  ggcyto_par_set(limits = list(x = c(-10000, 4000), y = c(-1000, 4500)))

Lower left within gate (location="gate" is default and could be left out here)

ggcyto(gs[[1]], aes("CD4", "CD8"), subset = "CD3+") +
  geom_hex(bins = 0) +
  geom_gate("CD4") +
  geom_stats(adjust = c(0.1, 0.1), location = "gate") +
  ggcyto_par_set(limits = list(x = c(-10000, 4000), y = c(-1000, 4500)))

Lower left within data range

ggcyto(gs[[1]], aes("CD4", "CD8"), subset = "CD3+") +
  geom_hex(bins = 0) +
  geom_gate("CD4") +
  geom_stats(adjust = c(0.1, 0.1), location = "data") +
  ggcyto_par_set(limits = list(x = c(-10000, 4000), y = c(-1000, 4500)))

Lower left within range of plot axis limits

ggcyto(gs[[1]], aes("CD4", "CD8"), subset = "CD3+") +
  geom_hex(bins = 0) +
  geom_gate("CD4") +
  geom_stats(adjust = c(0.1, 0.1), location = "plot") +
  ggcyto_par_set(limits = list(x = c(-10000, 4000), y = c(-1000, 4500)))

Fixed location

ggcyto(gs[[1]], aes("CD4", "CD8"), subset = "CD3+") +
  geom_hex(bins = 0) +
  geom_gate("CD4") +
  geom_stats(adjust = c(-2500, 2000), location = "fixed") +
  ggcyto_par_set(limits = list(x = c(-10000, 4000), y = c(-1000, 4500)))

Of course, there's also nothing really stopping you from pushing the annotation outside of whatever window by going beyond 1.0 or below 0.0. For example:

ggcyto(gs[[1]], aes("CD4", "CD8"), subset = "CD3+") +
  geom_hex(bins = 0) +
  geom_gate("CD4") +
  geom_stats(adjust = c(-0.5, 1.2), location = "gate") +
  ggcyto_par_set(limits = list(x = c(-10000, 4000), y = c(-1000, 4500)))

[alexheubeck]

Thanks @jacobpwagner, this is perfect. To that last point, I set the adjust annotation higher than 1 if I want the label outside of the gate pretty frequently. It would be good to mention that in the documentation.

[jacobpwagner]

Agreed. I actually meant to do that and then forgot. Now it's included.

[alexheubeck]

Looks like the location annotation works for regular gates, but it's not working for the boolean NOT gate that I'd like to use it for.

Using this line:

NKCells <- ggcyto(gs[[idx]], aes(x = CD14, y = CD56), subset = "CD3-CD19- Cells") + geom_hex(binwidth = c(0.015,0.015)) + ggcyto_par_set(limits = list(x = c(0.25,4.7), y = c(0.3,4.5))) + geom_gate(c('NK Cells'),col='black') + geom_stats('NK Cells',type = c("gate_name", "percent"), location = 'fixed', adjust=c(0.5,3), size=1.4, fill="transparent") ..

The label is placed properly:

Using this line, where the "CD3-CD19-CD56- Cells" gate is a boolean NOT gate of the "NK Cells" gate:

NKCells <- ggcyto(gs[[idx]], aes(x = CD14, y = CD56), subset = "CD3-CD19- Cells") + geom_hex(binwidth = c(0.015,0.015)) + ggcyto_par_set(limits = list(x = c(0.25,4.7), y = c(0.3,4.5))) + geom_gate(c('CD3-CD19-CD56- Cells'),col='black') + geom_stats('CD3-CD19-CD56- Cells',type = c("gate_name", "percent"), location = 'fixed', adjust=c(0.5,3), size=1.4, fill="transparent") ...

I get this error:

Error in FUN(X[[i]], ...) : object 'BUV661-A' not found

Where BUV661-A is the channel for x axis in this plot

[jacobpwagner]

Sorry about that. I think I know the issue. I'll try to get it fixed quickly.

[jacobpwagner]

@alexheubeck , will you try again after 333c61f? I think that should solve the issue. Note that for booleanFilter, the location="gate" option still gets automatically flipped to location="data". That is just a continuation of the prior behavior until more sophisticated logic is added there.

[alexheubeck]

@jacobpwagner, It's working now. Thank you once again for your help with this!