From 128d8b93255b229896267ff723fa417c4d55abc7 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Tue, 21 May 2024 16:50:00 -0400
Subject: [PATCH] fix examples for createCrossSection and addHMRF

---
 R/cross_section.R         | 13 +++++++++++--
 R/python_hmrf.R           | 25 +++++++++++++++++++++----
 man/addHMRF.Rd            | 25 +++++++++++++++++++++----
 man/createCrossSection.Rd | 13 +++++++++++--
 4 files changed, 64 insertions(+), 12 deletions(-)

diff --git a/R/cross_section.R b/R/cross_section.R
index 873a88047..5d0dcb0d9 100644
--- a/R/cross_section.R
+++ b/R/cross_section.R
@@ -522,9 +522,18 @@ create_mesh_grid_lines <- function(
 #' network object. The users need to provide the definition of the cross
 #' section plane (see method).
 #' @examples
-#' g <- GiottoData::loadGiottoMini("visium")
+#' g <- GiottoData::loadGiottoMini("starmap")
 #'
-#' createCrossSection(gobject = g, spatial_network_name = "spatial_network")
+#' g <- createCrossSection(
+#'     gobject = g,
+#'     method = "equation",
+#'     equation=c(0,1,0,600),
+#'     extend_ratio = 0.6,
+#'     name = "new_cs",
+#'     return_gobject = TRUE
+#' )
+#'
+#' crossSectionPlot(g, name = "new_cs")
 #' @export
 createCrossSection <- function(gobject,
     spat_unit = NULL,
diff --git a/R/python_hmrf.R b/R/python_hmrf.R
index fa11c4a75..2f7504179 100644
--- a/R/python_hmrf.R
+++ b/R/python_hmrf.R
@@ -555,11 +555,28 @@ writeHMRFresults <- function(gobject,
 #' g <- GiottoData::loadGiottoMini("visium")
 #' spat_genes <- binSpect(g)
 #'
-#' output_folder <- tempdir()
-#' doHMRF(g, spatial_genes = spat_genes[seq_len(10)]$feats,
-#' output_folder = output_folder)
+#' output_folder <- file.path(tempdir(), 'HMRF')
+#' if(!file.exists(output_folder)) dir.create(output_folder, recursive = TRUE)
+#'
+#' out <- doHMRF(
+#'     g, spatial_genes = spat_genes[seq_len(20)]$feats,
+#'     expression_values = "scaled",
+#'     spatial_network_name = "Delaunay_network",
+#'     k = 6, betas = c(0, 10, 5),
+#'     output_folder = output_folder
+#' )
+#'
+#' g <- addHMRF(
+#'     gobject = g,
+#'     HMRFoutput = out,
+#'     k = 6,
+#'     betas_to_add = 20,
+#'     hmrf_name = "HMRF"
+#' )
 #'
-#' addHMRF(gobject = g, HMRFoutput = doHMRF)
+#' spatPlot(
+#'     gobject = g, cell_color = 'HMRF_k6_b.20',
+#' )
 #' @export
 addHMRF <- function(gobject,
     spat_unit = NULL,
diff --git a/man/addHMRF.Rd b/man/addHMRF.Rd
index d2aff7dbc..6a751fa6d 100644
--- a/man/addHMRF.Rd
+++ b/man/addHMRF.Rd
@@ -39,9 +39,26 @@ Add selected results from doHMRF to the giotto object
 g <- GiottoData::loadGiottoMini("visium")
 spat_genes <- binSpect(g)
 
-output_folder <- tempdir()
-doHMRF(g, spatial_genes = spat_genes[seq_len(10)]$feats,
-output_folder = output_folder)
+output_folder <- file.path(tempdir(), 'HMRF')
+if(!file.exists(output_folder)) dir.create(output_folder, recursive = TRUE)
 
-addHMRF(gobject = g, HMRFoutput = doHMRF)
+out <- doHMRF(
+    g, spatial_genes = spat_genes[seq_len(20)]$feats,
+    expression_values = "scaled",
+    spatial_network_name = "Delaunay_network",
+    k = 6, betas = c(0, 10, 5),
+    output_folder = output_folder
+)
+
+g <- addHMRF(
+    gobject = g,
+    HMRFoutput = out,
+    k = 6,
+    betas_to_add = 20,
+    hmrf_name = "HMRF"
+)
+
+spatPlot(
+    gobject = g, cell_color = 'HMRF_k6_b.20',
+)
 }
diff --git a/man/createCrossSection.Rd b/man/createCrossSection.Rd
index 4f538c67c..c80dce48b 100644
--- a/man/createCrossSection.Rd
+++ b/man/createCrossSection.Rd
@@ -106,7 +106,16 @@ network object. The users need to provide the definition of the cross
 section plane (see method).
 }
 \examples{
-g <- GiottoData::loadGiottoMini("visium")
+g <- GiottoData::loadGiottoMini("starmap")
+
+g <- createCrossSection(
+    gobject = g,
+    method = "equation",
+    equation=c(0,1,0,600),
+    extend_ratio = 0.6,
+    name = "new_cs",
+    return_gobject = TRUE
+)
 
-createCrossSection(gobject = g, spatial_network_name = "spatial_network")
+crossSectionPlot(g, name = "new_cs")
 }