From a6f5b3bdb814181ba5ba0a00fe247fa0346c1b38 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Wed, 29 Jun 2022 18:31:50 +0100
Subject: [PATCH] feat(imageviewer): add visualisation options
---
aliby/utils/imageViewer.py | 59 ++++++++++++++++++++++++++++----------
1 file changed, 44 insertions(+), 15 deletions(-)
diff --git a/aliby/utils/imageViewer.py b/aliby/utils/imageViewer.py
index 974180c1..5d7a5d44 100644
--- a/aliby/utils/imageViewer.py
+++ b/aliby/utils/imageViewer.py
@@ -357,23 +357,52 @@ class remoteImageViewer:
)
custom_imshow(
tiled_imgs["cell_labels"],
- cmap="Set1",
+ cmap=sns.color_palette("Paired", as_cmap=True),
**lbl_plot_kwargs,
)
- plt.yticks(
- ticks=[
- (i * self.tiler.tile_size * nrows)
- + self.tiler.tile_size * nrows / 2
- for i in range(len(channels))
- ],
- labels=channel_labels,
- )
- plt.xticks(
- ticks=[self.tiler.tile_size * (i + 0.5) for i in range(ncols)],
- labels=["+ {} ".format(i) for i in range(ncols)],
- )
- plt.xlabel("Additional time-points")
- plt.show()
+
+ if remove_axis == True:
+ plt.axis("off")
+ elif remove_axis == "x":
+ plt.tick_params(
+ axis="x",
+ which="both",
+ bottom=False,
+ top=False,
+ labelbottom=False,
+ )
+
+ if remove_axis != "True":
+ plt.yticks(
+ ticks=[
+ (i * self.tiler.tile_size * nrows)
+ + self.tiler.tile_size * nrows / 2
+ for i in range(len(channels))
+ ],
+ labels=channel_labels,
+ )
+
+ if not remove_axis:
+ xlabels = (
+ ["+ {} ".format(i) for i in range(ncols)]
+ if nrows > 1
+ else list(trange)
+ )
+ plt.xlabel("Time-point")
+
+ plt.xticks(
+ ticks=[self.tiler.tile_size * (i + 0.5) for i in range(ncols)],
+ labels=xlabels,
+ )
+
+ if not np.any(out):
+ print("ImageViewer:Warning:No cell outlines found")
+
+ if savefile:
+ plt.savefig(savefile, bbox_inches="tight", dpi=300)
+ plt.close()
+ else:
+ plt.show()
# def plot_labelled_trap(
# self,
--
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