... | ... |
@@ -72,9 +72,9 @@ Expression Histology, using the |
72 | 72 |
\href{https://github.com/Teichlab/SpatialDE}{\strong{SpatialDE}} Python package. |
73 | 73 |
} |
74 | 74 |
\examples{ |
75 |
-## Mock up a SpatialExperiment object wit 25 cells, 100 genes |
|
75 |
+## Mock up a SpatialExperiment object wit 100 cells and 3 genes |
|
76 | 76 |
set.seed(42) |
77 |
-spe <- mockSVG(size = 5, tot_genes = 100, de_genes = 10, return_SPE = TRUE) |
|
77 |
+spe <- mockSVG(size = 10, tot_genes = 3, de_genes = 1, return_SPE = TRUE) |
|
78 | 78 |
|
79 | 79 |
## Run spatialDE |
80 | 80 |
de_results <- spatialDE(spe) |
... | ... |
@@ -72,9 +72,9 @@ Expression Histology, using the |
72 | 72 |
\href{https://github.com/Teichlab/SpatialDE}{\strong{SpatialDE}} Python package. |
73 | 73 |
} |
74 | 74 |
\examples{ |
75 |
-## Mock up a SpatialExperiment object wit 100 cells, 200 genes |
|
75 |
+## Mock up a SpatialExperiment object wit 25 cells, 100 genes |
|
76 | 76 |
set.seed(42) |
77 |
-spe <- mockSVG(size = 10, tot_genes = 200, de_genes = 20, return_SPE = TRUE) |
|
77 |
+spe <- mockSVG(size = 5, tot_genes = 100, de_genes = 10, return_SPE = TRUE) |
|
78 | 78 |
|
79 | 79 |
## Run spatialDE |
80 | 80 |
de_results <- spatialDE(spe) |
... | ... |
@@ -101,5 +101,5 @@ The individual steps performed by this function: \code{\link[=stabilize]{stabili |
101 | 101 |
\code{\link[=regress_out]{regress_out()}} and \code{\link[=spatial_patterns]{spatial_patterns()}}. |
102 | 102 |
} |
103 | 103 |
\author{ |
104 |
-Davide Corso, Milan Malfait |
|
104 |
+Davide Corso, Milan Malfait, Lambda Moses |
|
105 | 105 |
} |
... | ... |
@@ -2,30 +2,46 @@ |
2 | 2 |
% Please edit documentation in R/aeh.R |
3 | 3 |
\name{spatialPatterns} |
4 | 4 |
\alias{spatialPatterns} |
5 |
+\alias{spatialPatterns,matrix-method} |
|
5 | 6 |
\alias{spatialPatterns,SpatialExperiment-method} |
6 | 7 |
\title{Automatic expression histology in \strong{SpatialDE}} |
7 | 8 |
\usage{ |
8 | 9 |
spatialPatterns(x, de_results, ...) |
9 | 10 |
|
11 |
+\S4method{spatialPatterns}{matrix}( |
|
12 |
+ x, |
|
13 |
+ de_results, |
|
14 |
+ coordinates, |
|
15 |
+ qval_thresh = 0.05, |
|
16 |
+ n_patterns, |
|
17 |
+ length, |
|
18 |
+ verbose = FALSE |
|
19 |
+) |
|
20 |
+ |
|
10 | 21 |
\S4method{spatialPatterns}{SpatialExperiment}( |
11 | 22 |
x, |
12 | 23 |
de_results, |
13 |
- assay_type = "counts", |
|
14 | 24 |
qval_thresh = 0.05, |
15 | 25 |
n_patterns, |
16 | 26 |
length, |
27 |
+ assay_type = "counts", |
|
17 | 28 |
verbose = FALSE |
18 | 29 |
) |
19 | 30 |
} |
20 | 31 |
\arguments{ |
21 |
-\item{x}{\linkS4class{SpatialExperiment} object.} |
|
32 |
+\item{x}{A numeric \code{matrix} of counts where genes are rows and cells are columns. |
|
33 |
+ |
|
34 |
+Alternatively, a \linkS4class{SpatialExperiment} object.} |
|
22 | 35 |
|
23 | 36 |
\item{de_results}{\code{data.frame} resulting from \code{\link[=run]{run()}} or \code{\link[=spatialDE]{spatialDE()}}.} |
24 | 37 |
|
25 | 38 |
\item{...}{For the generic, arguments to pass to specific methods.} |
26 | 39 |
|
27 |
-\item{assay_type}{A \code{character} string specifying the assay from \code{x} to use |
|
28 |
-as input. Defaults to \code{"counts"}.} |
|
40 |
+\item{coordinates}{A \code{data.frame} with sample coordinates. Each row is a |
|
41 |
+sample, the columns with coordinates should be named 'x' and 'y'. |
|
42 |
+ |
|
43 |
+For the \emph{SpatialExperiment} method, coordinates are taken from |
|
44 |
+\code{spatialCoords(x)}.} |
|
29 | 45 |
|
30 | 46 |
\item{qval_thresh}{\code{numeric} scalar, specifying the q-value significance |
31 | 47 |
threshold to filter \code{de_results}. Only rows in \code{de_results} with |
... | ... |
@@ -37,6 +53,9 @@ threshold to filter \code{de_results}. Only rows in \code{de_results} with |
37 | 53 |
|
38 | 54 |
\item{verbose}{A \code{logical} controlling the display of a progress bar from the |
39 | 55 |
Python package.} |
56 |
+ |
|
57 |
+\item{assay_type}{A \code{character} string specifying the assay from \code{x} to use |
|
58 |
+as input. Defaults to \code{"counts"}.} |
|
40 | 59 |
} |
41 | 60 |
\value{ |
42 | 61 |
A \code{list} of two \code{data.frame}s (pattern_results, patterns): |
This argument should always be present for specific methods of `spatialPatterns()` and `modelSearch()`
... | ... |
@@ -5,12 +5,12 @@ |
5 | 5 |
\alias{spatialPatterns,SpatialExperiment-method} |
6 | 6 |
\title{Automatic expression histology in \strong{SpatialDE}} |
7 | 7 |
\usage{ |
8 |
-spatialPatterns(x, ...) |
|
8 |
+spatialPatterns(x, de_results, ...) |
|
9 | 9 |
|
10 | 10 |
\S4method{spatialPatterns}{SpatialExperiment}( |
11 | 11 |
x, |
12 |
- assay_type = "counts", |
|
13 | 12 |
de_results, |
13 |
+ assay_type = "counts", |
|
14 | 14 |
qval_thresh = 0.05, |
15 | 15 |
n_patterns, |
16 | 16 |
length, |
... | ... |
@@ -20,13 +20,13 @@ spatialPatterns(x, ...) |
20 | 20 |
\arguments{ |
21 | 21 |
\item{x}{\linkS4class{SpatialExperiment} object.} |
22 | 22 |
|
23 |
+\item{de_results}{\code{data.frame} resulting from \code{\link[=run]{run()}} or \code{\link[=spatialDE]{spatialDE()}}.} |
|
24 |
+ |
|
23 | 25 |
\item{...}{For the generic, arguments to pass to specific methods.} |
24 | 26 |
|
25 | 27 |
\item{assay_type}{A \code{character} string specifying the assay from \code{x} to use |
26 | 28 |
as input. Defaults to \code{"counts"}.} |
27 | 29 |
|
28 |
-\item{de_results}{\code{data.frame} resulting from \code{\link[=run]{run()}} or \code{\link[=spatialDE]{spatialDE()}}.} |
|
29 |
- |
|
30 | 30 |
\item{qval_thresh}{\code{numeric} scalar, specifying the q-value significance |
31 | 31 |
threshold to filter \code{de_results}. Only rows in \code{de_results} with |
32 | 32 |
\code{qval < qval_thresh} will be kept. To disable, set \code{qval_thresh = NULL}.} |
1 | 1 |
new file mode 100644 |
... | ... |
@@ -0,0 +1,86 @@ |
1 |
+% Generated by roxygen2: do not edit by hand |
|
2 |
+% Please edit documentation in R/aeh.R |
|
3 |
+\name{spatialPatterns} |
|
4 |
+\alias{spatialPatterns} |
|
5 |
+\alias{spatialPatterns,SpatialExperiment-method} |
|
6 |
+\title{Automatic expression histology in \strong{SpatialDE}} |
|
7 |
+\usage{ |
|
8 |
+spatialPatterns(x, ...) |
|
9 |
+ |
|
10 |
+\S4method{spatialPatterns}{SpatialExperiment}( |
|
11 |
+ x, |
|
12 |
+ assay_type = "counts", |
|
13 |
+ de_results, |
|
14 |
+ qval_thresh = 0.05, |
|
15 |
+ n_patterns, |
|
16 |
+ length, |
|
17 |
+ verbose = FALSE |
|
18 |
+) |
|
19 |
+} |
|
20 |
+\arguments{ |
|
21 |
+\item{x}{\linkS4class{SpatialExperiment} object.} |
|
22 |
+ |
|
23 |
+\item{...}{For the generic, arguments to pass to specific methods.} |
|
24 |
+ |
|
25 |
+\item{assay_type}{A \code{character} string specifying the assay from \code{x} to use |
|
26 |
+as input. Defaults to \code{"counts"}.} |
|
27 |
+ |
|
28 |
+\item{de_results}{\code{data.frame} resulting from \code{\link[=run]{run()}} or \code{\link[=spatialDE]{spatialDE()}}.} |
|
29 |
+ |
|
30 |
+\item{qval_thresh}{\code{numeric} scalar, specifying the q-value significance |
|
31 |
+threshold to filter \code{de_results}. Only rows in \code{de_results} with |
|
32 |
+\code{qval < qval_thresh} will be kept. To disable, set \code{qval_thresh = NULL}.} |
|
33 |
+ |
|
34 |
+\item{n_patterns}{\code{integer} The number of spatial patterns} |
|
35 |
+ |
|
36 |
+\item{length}{\code{numeric} The characteristic length scale of the clusters} |
|
37 |
+ |
|
38 |
+\item{verbose}{A \code{logical} controlling the display of a progress bar from the |
|
39 |
+Python package.} |
|
40 |
+} |
|
41 |
+\value{ |
|
42 |
+A \code{list} of two \code{data.frame}s (pattern_results, patterns): |
|
43 |
+\itemize{ |
|
44 |
+\item \code{pattern_results}: \code{data.frame} with pattern membership information for each |
|
45 |
+gene. |
|
46 |
+\item \code{patterns} the posterior mean underlying expression from genes in given |
|
47 |
+spatial patterns. |
|
48 |
+} |
|
49 |
+} |
|
50 |
+\description{ |
|
51 |
+Group spatially variable genes into spatial patterns using Automatic |
|
52 |
+Expression Histology, using the |
|
53 |
+\href{https://github.com/Teichlab/SpatialDE}{\strong{SpatialDE}} Python package. |
|
54 |
+} |
|
55 |
+\examples{ |
|
56 |
+## Mock up a SpatialExperiment object wit 100 cells, 200 genes |
|
57 |
+set.seed(42) |
|
58 |
+spe <- mockSVG(size = 10, tot_genes = 200, de_genes = 20, return_SPE = TRUE) |
|
59 |
+ |
|
60 |
+## Run spatialDE |
|
61 |
+de_results <- spatialDE(spe) |
|
62 |
+ |
|
63 |
+spatial_patterns <- spatialPatterns(spe, de_results = de_results, |
|
64 |
+ qval_thresh = NULL, n_patterns = 4L, length = 1.5, |
|
65 |
+ verbose = FALSE |
|
66 |
+) |
|
67 |
+ |
|
68 |
+head(spatial_patterns$pattern_results) |
|
69 |
+head(spatial_patterns$patterns) |
|
70 |
+ |
|
71 |
+} |
|
72 |
+\references{ |
|
73 |
+Svensson, V., Teichmann, S. & Stegle, O. SpatialDE: identification of |
|
74 |
+spatially variable genes. Nat Methods 15, 343–346 (2018). |
|
75 |
+\url{https://doi.org/10.1038/nmeth.4636} |
|
76 |
+ |
|
77 |
+\href{https://pypi.org/project/SpatialDE/1.1.3/}{\strong{SpatialDE 1.1.3}}: the version |
|
78 |
+of the Python package used under the hood. |
|
79 |
+} |
|
80 |
+\seealso{ |
|
81 |
+The individual steps performed by this function: \code{\link[=stabilize]{stabilize()}}, |
|
82 |
+\code{\link[=regress_out]{regress_out()}} and \code{\link[=spatial_patterns]{spatial_patterns()}}. |
|
83 |
+} |
|
84 |
+\author{ |
|
85 |
+Davide Corso, Milan Malfait |
|
86 |
+} |