VisualizeHeatmap: Visualize spot values on the 2D slide

In zijianni/SpotClean: SpotClean adjusts for spot swapping in spatial transcriptomics data

Visualize spot values on the 2D slide

Description

Generate and visualize spot labels on the 2D slide as a ggplot2 object. Spot labels can be given via parameter label as external input or one column in the slide slot of the slide object's metadata via label_col. Exactly one of label and label_col must be specified.

Usage

visualizeHeatmap(object, ...)

## Default S3 method:
visualizeHeatmap(
  object,
  value,
  exp_matrix = NULL,
  subset_barcodes = NULL,
  logged = TRUE,
  viridis = TRUE,
  legend_range = NULL,
  title = "",
  legend_title = NULL,
  ...
)

## S3 method for class 'SummarizedExperiment'
visualizeHeatmap(
  object,
  value,
  subset_barcodes = NULL,
  logged = TRUE,
  viridis = TRUE,
  legend_range = NULL,
  title = "",
  legend_title = NULL,
  ...
)

Arguments

object	A slide object created or inherited from createSlide(), or a data.frame of slide information with columns: barcodes, tissue, imagerow, imagecol, etc.
...	Arguments passed to other methods
value	(numeric vector or chr) Either a vector of numeric values for all spots, or the name of one gene in exp_matrix or in the expression matrix in the slide object. In the former case, the order of values in the vector should match the spot barcodes in the slide object.
exp_matrix	(matrix of num) When object is a data frame and value is a single character string, will search the matching gene in exp_matrix and plot the gene expression. Default: NULL
subset_barcodes	(vector of chr) A subset of spot barcodes to plot. By default it plots all spots in the slide object. This can be useful when only plotting tissue spots or specific tissue types or regions. Default: NULL
logged	(logical) Specify if the color scale is log1p transformed. Default: TRUE
viridis	(logical) If true, color scale uses viridis. Otherwise, use rainbow. Default: TRUE
legend_range	(length 2 vector of num) Custom legend range of the value. By default uses the range of the plotted values. Default: NULL
title	(chr) Title of the plot. Default: ""
legend_title	(chr) Title of the legend. Under default, use value as legend title. Default: NULL

Value

A ggplot2 object.

Examples

data(mbrain_raw)
spatial_dir <- system.file(file.path("extdata",
                                     "V1_Adult_Mouse_Brain_spatial"),
                           package = "SpotClean")
mbrain_slide_info <- read10xSlide(tissue_csv_file=file.path(spatial_dir,
                                       "tissue_positions_list.csv"),
             tissue_img_file = file.path(spatial_dir,
                                       "tissue_lowres_image.png"),
             scale_factor_file = file.path(spatial_dir,
                                       "scalefactors_json.json"))
mbrain_obj <- createSlide(mbrain_raw,
                          mbrain_slide_info)

gp <- visualizeHeatmap(mbrain_obj, "Bc1",
                     title="mbrain", legend_title="Bc1 expression")
plot(gp)

zijianni/SpotClean documentation built on Nov. 15, 2023, 12:53 a.m.