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Preprocessed MERFISH dataset of the mouse preoptic area for a bregma -0.29 slice from a female naive animal (Animal ID = 1).
+Preprocessed MERFISH dataset of the mouse preoptic area for a bregma -0.29 slice from a female naive animal (Animal ID = 1, Animal Sex = "Female", # Behavior = "Naive", Bregma = "-0.29").
Source:R/data.R
merfish_mousePOA.RdPreprocessed MERFISH dataset of the mouse preoptic area for a bregma -0.29 slice -from a female naive animal (Animal ID = 1).
+from a female naive animal (Animal ID = 1, Animal Sex = "Female", +# Behavior = "Naive", Bregma = "-0.29").
diff --git a/docs/reference/permutateByRotation.html b/docs/reference/permutateByRotation.html
index f7de709..257733d 100644
--- a/docs/reference/permutateByRotation.html
+++ b/docs/reference/permutateByRotation.html
@@ -134,7 +134,8 @@ Examples
Examplesdata("merfish_mousePOA")
# create a list of 3 permutated datasets rotated at 0 (original), 120, and 240 degrees
-# this output can directly be fed into rasterizeGeneExpression or rasterizeCellType functions to rasterize all 3 permutations at once with the same pixel coordinates
+# this output can directly be fed into rasterizeGeneExpression or rasterizeCellType
+# functions to rasterize all 3 permutations at once with the same pixel coordinates
spe_list <- permutateByRotation(merfish_mousePOA, n_perm = 3)
# create a list of 5 permutated datasets rotated at 0 (original), 72, 144, 216, 288 degrees
diff --git a/docs/reference/plotRaster.html b/docs/reference/plotRaster.html
index 7e3dcee..b161da4 100644
--- a/docs/reference/plotRaster.html
+++ b/docs/reference/plotRaster.html
@@ -148,34 +148,32 @@ Examples
# rasterize gene expression
out <- rasterizeGeneExpression(merfish_mousePOA, assay_name = "volnorm", fun = "mean")
+#> Error in 0:nx: NA/NaN argument
-# plot total rasterized gene expression per pixel (there is only one assay_name in out and default for feature_name argument is "sum"; therefore, these arguments are not specified)
+# plot total rasterized gene expression per pixel (there is only one assay_name
+# in out and default for feature_name argument is "sum"; therefore, these arguments
+# are not specified)
plotRaster(out, name = "total rasterized gexp")
-#> Coordinate system already present. Adding new coordinate system, which will
-#> replace the existing one.
-
+#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'assay': object 'out' not found
# plot rasterized expression of a specific gene/feature per pixel
plotRaster(out, feature_name = "Esr1", name = "Esr1")
-#> Coordinate system already present. Adding new coordinate system, which will
-#> replace the existing one.
-
+#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'assay': object 'out' not found
# rasterize cell-type labels with user-defined resolution and hexagonal pixels
out <- rasterizeCellType(merfish_mousePOA, col_name = "celltype", resolution = 50, square = FALSE, fun = "sum")
+#> Error in seq.default(xlim[1] - dx, xlim[2] + 2 * dx, dx): 'from' must be a finite number
-# plot total cell counts per pixel (there is only one assay_name in out and default for feature_name argument is "sum"; therefore, these arguments are not specified)
-# here, let's use additional parameters for ggplot2::scale_fill_viridis_c so that it would have a different color scheme from gene expression plots
+# plot total cell counts per pixel (there is only one assay_name in out and default
+# for feature_name argument is "sum"; therefore, these arguments are not specified)
+# here, let's use additional parameters for ggplot2::scale_fill_viridis_c so
+# that it would have a different color scheme from gene expression plots
plotRaster(out, name = "total cell counts", option = "inferno")
-#> Coordinate system already present. Adding new coordinate system, which will
-#> replace the existing one.
-
+#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'assay': object 'out' not found
# plot specific cell type's cell counts per pixel
plotRaster(out, feature_name = "Inhibitory", name = "Inhibitory neuron counts", option = "inferno")
-#> Coordinate system already present. Adding new coordinate system, which will
-#> replace the existing one.
-
+#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'assay': object 'out' not found
data("merfish_mousePOA")
# create a list of 3 permutated datasets rotated at 0 (original), 120, and 240 degrees
-# this output can directly be fed into rasterizeGeneExpression or rasterizeCellType functions to rasterize all 3 permutations at once with the same pixel coordinates
+# this output can directly be fed into rasterizeGeneExpression or rasterizeCellType
+# functions to rasterize all 3 permutations at once with the same pixel coordinates
spe_list <- permutateByRotation(merfish_mousePOA, n_perm = 3)
# create a list of 5 permutated datasets rotated at 0 (original), 72, 144, 216, 288 degrees
diff --git a/docs/reference/plotRaster.html b/docs/reference/plotRaster.html
index 7e3dcee..b161da4 100644
--- a/docs/reference/plotRaster.html
+++ b/docs/reference/plotRaster.html
@@ -148,34 +148,32 @@ Examples
# rasterize gene expression
out <- rasterizeGeneExpression(merfish_mousePOA, assay_name = "volnorm", fun = "mean")
+#> Error in 0:nx: NA/NaN argument
-# plot total rasterized gene expression per pixel (there is only one assay_name in out and default for feature_name argument is "sum"; therefore, these arguments are not specified)
+# plot total rasterized gene expression per pixel (there is only one assay_name
+# in out and default for feature_name argument is "sum"; therefore, these arguments
+# are not specified)
plotRaster(out, name = "total rasterized gexp")
-#> Coordinate system already present. Adding new coordinate system, which will
-#> replace the existing one.
-
+#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'assay': object 'out' not found
# plot rasterized expression of a specific gene/feature per pixel
plotRaster(out, feature_name = "Esr1", name = "Esr1")
-#> Coordinate system already present. Adding new coordinate system, which will
-#> replace the existing one.
-
+#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'assay': object 'out' not found
# rasterize cell-type labels with user-defined resolution and hexagonal pixels
out <- rasterizeCellType(merfish_mousePOA, col_name = "celltype", resolution = 50, square = FALSE, fun = "sum")
+#> Error in seq.default(xlim[1] - dx, xlim[2] + 2 * dx, dx): 'from' must be a finite number
-# plot total cell counts per pixel (there is only one assay_name in out and default for feature_name argument is "sum"; therefore, these arguments are not specified)
-# here, let's use additional parameters for ggplot2::scale_fill_viridis_c so that it would have a different color scheme from gene expression plots
+# plot total cell counts per pixel (there is only one assay_name in out and default
+# for feature_name argument is "sum"; therefore, these arguments are not specified)
+# here, let's use additional parameters for ggplot2::scale_fill_viridis_c so
+# that it would have a different color scheme from gene expression plots
plotRaster(out, name = "total cell counts", option = "inferno")
-#> Coordinate system already present. Adding new coordinate system, which will
-#> replace the existing one.
-
+#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'assay': object 'out' not found
# plot specific cell type's cell counts per pixel
plotRaster(out, feature_name = "Inhibitory", name = "Inhibitory neuron counts", option = "inferno")
-#> Coordinate system already present. Adding new coordinate system, which will
-#> replace the existing one.
-
+#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'assay': object 'out' not found