Visualizes data using various plot types such as bar plots, rose plots, ring plots, pie charts, trend plots, area plots, dot plots, sankey plots, chord plots, venn diagrams, and upset plots.
Usage
StatPlot(
meta.data,
stat.by,
group.by = NULL,
split.by = NULL,
bg.by = NULL,
flip = FALSE,
NA_color = "grey",
NA_stat = TRUE,
keep_empty = FALSE,
individual = FALSE,
stat_level = NULL,
plot_type = c("bar", "rose", "ring", "pie", "trend", "area", "dot", "sankey", "chord",
"venn", "upset"),
stat_type = c("percent", "count"),
position = c("stack", "dodge"),
palette = "Paired",
palcolor = NULL,
alpha = 1,
bg_palette = "Paired",
bg_palcolor = NULL,
bg_alpha = 0.2,
label = FALSE,
label.size = 3.5,
label.fg = "black",
label.bg = "white",
label.bg.r = 0.1,
aspect.ratio = NULL,
title = NULL,
subtitle = NULL,
xlab = NULL,
ylab = NULL,
legend.position = "right",
legend.direction = "vertical",
theme_use = "theme_scop",
theme_args = list(),
combine = TRUE,
nrow = NULL,
ncol = NULL,
byrow = TRUE,
force = FALSE,
seed = 11
)
Arguments
- meta.data
The data frame containing the data to be plotted.
- stat.by
The column name(s) in
meta.data
specifying the variable(s) to be plotted.- group.by
The column name in
meta.data
specifying the grouping variable.- split.by
The column name in
meta.data
specifying the splitting variable.- bg.by
The column name in
meta.data
specifying the background variable for bar plots.- flip
Logical indicating whether to flip the plot.
- NA_color
The color to use for missing values.
- NA_stat
Logical indicating whether to include missing values in the plot.
- keep_empty
Logical indicating whether to keep empty groups in the plot.
- individual
Logical indicating whether to plot individual groups separately.
- stat_level
The level(s) of the variable(s) specified in
stat.by
to include in the plot.- plot_type
The type of plot to create. Can be one of "bar", "rose", "ring", "pie", "trend", "area", "dot", "sankey", "chord", "venn", or "upset".
- stat_type
The type of statistic to compute for the plot. Can be one of "percent" or "count".
- position
The position adjustment for the plot. Can be one of "stack" or "dodge".
- palette
The name of the color palette to use for the plot.
- palcolor
The color to use in the color palette.
- alpha
The transparency level for the plot.
- bg_palette
The name of the background color palette to use for bar plots.
- bg_palcolor
The color to use in the background color palette.
- bg_alpha
The transparency level for the background color in bar plots.
- label
Logical indicating whether to add labels on the plot.
- label.size
The size of the labels.
- label.fg
The foreground color of the labels.
- label.bg
The background color of the labels.
- label.bg.r
The radius of the rounded corners of the label background.
- aspect.ratio
The aspect ratio of the plot.
- title
The main title of the plot.
- subtitle
The subtitle of the plot.
- xlab
The x-axis label of the plot.
- ylab
The y-axis label of the plot.
- legend.position
The position of the legend in the plot. Can be one of "right", "left", "bottom", "top", or "none".
- legend.direction
The direction of the legend in the plot. Can be one of "vertical" or "horizontal".
- theme_use
The name of the theme to use for the plot. Can be one of the predefined themes or a custom theme.
- theme_args
A list of arguments to be passed to the theme function.
- combine
Logical indicating whether to combine multiple plots into a single plot.
- nrow
The number of rows in the combined plot.
- ncol
The number of columns in the combined plot.
- byrow
Logical indicating whether to fill the plot by row or by column.
- force
Logical indicating whether to force the plot even if some variables have more than 100 levels.
- seed
The random seed to use for reproducible results.
Examples
data(pancreas_sub)
head(pancreas_sub@meta.data)
#> orig.ident nCount_RNA nFeature_RNA S_score G2M_score
#> AAACCTGAGCCTTGAT SeuratProject 7071 2613 -0.01470664 -0.23261042
#> AAACCTGAGGCAATTA SeuratProject 4070 1984 -0.17125480 -0.28683382
#> AAACCTGTCTTTCCTC SeuratProject 9592 3410 0.55623430 -0.05274934
#> AAACGGGAGATATGGT SeuratProject 6194 2486 -0.16794573 -0.16668808
#> AAACGGGCAAGGACAC SeuratProject 10490 3281 0.21798572 0.68136787
#> AAACGGGCAGTTCCCT SeuratProject 6342 2430 -0.15680908 -0.16858186
#> nCount_spliced nFeature_spliced nCount_unspliced
#> AAACCTGAGCCTTGAT 7071 2613 959
#> AAACCTGAGGCAATTA 4070 1984 1076
#> AAACCTGTCTTTCCTC 9592 3410 1339
#> AAACGGGAGATATGGT 6194 2486 728
#> AAACGGGCAAGGACAC 10490 3281 1441
#> AAACGGGCAGTTCCCT 6342 2430 1113
#> nFeature_unspliced CellType SubCellType Phase
#> AAACCTGAGCCTTGAT 643 Ductal Ductal G1
#> AAACCTGAGGCAATTA 701 Endocrine Alpha G1
#> AAACCTGTCTTTCCTC 894 Ductal Ductal S
#> AAACGGGAGATATGGT 556 Ductal Ductal G1
#> AAACGGGCAAGGACAC 1008 Ductal Ductal G2M
#> AAACGGGCAGTTCCCT 808 Ductal Ductal G1
StatPlot(
pancreas_sub@meta.data,
stat.by = "Phase",
group.by = "CellType",
plot_type = "bar",
label = TRUE
)
StatPlot(
pancreas_sub[["RNA"]]@meta.data,
stat.by = "highly_variable_genes",
plot_type = "ring",
label = TRUE,
NA_stat = FALSE
)
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_col()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_text_repel()`).
pancreas_sub <- AnnotateFeatures(
pancreas_sub,
species = "Mus_musculus",
IDtype = "symbol",
# db = c("VerSeDa", "TF")
db = "VerSeDa"
)
#> ℹ [2025-07-26 08:01:23] Species: Mus_musculus
#> ℹ [2025-07-26 08:01:24] Preparing database: VerSeDa
#> ℹ [2025-07-26 08:01:30] Connect to the Ensembl archives...
#> ℹ [2025-07-26 08:01:30] Using the 103 version of biomart...
#> ℹ [2025-07-26 08:01:30] Connecting to the biomart...
#> ℹ [2025-07-26 08:02:30] Error in `req_perform()`:
#> ℹ [2025-07-26 08:02:30] ! Failed to perform HTTP request.
#> ℹ [2025-07-26 08:02:30] Caused by error in `curl::curl_fetch_memory()`:
#> ℹ [2025-07-26 08:02:30] ! Timeout was reached [feb2021.archive.ensembl.org]:
#> ℹ [2025-07-26 08:02:30] Operation timed out after 60001 milliseconds with 0 bytes received
#> ℹ [2025-07-26 08:02:30]
#> ℹ [2025-07-26 08:02:30] Get errors when connecting with ensembl mart...
#> ℹ [2025-07-26 08:02:31] Retrying...
#> ℹ [2025-07-26 08:03:31] Error in `req_perform()`:
#> ℹ [2025-07-26 08:03:31] ! Failed to perform HTTP request.
#> ℹ [2025-07-26 08:03:31] Caused by error in `curl::curl_fetch_memory()`:
#> ℹ [2025-07-26 08:03:31] ! Timeout was reached [feb2021.archive.ensembl.org]:
#> ℹ [2025-07-26 08:03:31] Operation timed out after 60002 milliseconds with 0 bytes received
#> ℹ [2025-07-26 08:03:31]
#> ℹ [2025-07-26 08:03:31] Get errors when connecting with ensembl mart...
#> ℹ [2025-07-26 08:03:32] Retrying...
#> ℹ [2025-07-26 08:04:32] Error in `req_perform()`:
#> ℹ [2025-07-26 08:04:32] ! Failed to perform HTTP request.
#> ℹ [2025-07-26 08:04:32] Caused by error in `curl::curl_fetch_memory()`:
#> ℹ [2025-07-26 08:04:32] ! Timeout was reached [feb2021.archive.ensembl.org]:
#> ℹ [2025-07-26 08:04:32] Operation timed out after 60002 milliseconds with 0 bytes received
#> ℹ [2025-07-26 08:04:32]
#> ℹ [2025-07-26 08:04:32] Get errors when connecting with ensembl mart...
#> ℹ [2025-07-26 08:04:33] Retrying...
#> ℹ [2025-07-26 08:05:33] Error in `req_perform()`:
#> ℹ [2025-07-26 08:05:33] ! Failed to perform HTTP request.
#> ℹ [2025-07-26 08:05:33] Caused by error in `curl::curl_fetch_memory()`:
#> ℹ [2025-07-26 08:05:33] ! Timeout was reached [feb2021.archive.ensembl.org]:
#> ℹ [2025-07-26 08:05:33] Operation timed out after 60002 milliseconds with 0 bytes received
#> ℹ [2025-07-26 08:05:33]
#> ℹ [2025-07-26 08:05:33] Get errors when connecting with ensembl mart...
#> ℹ [2025-07-26 08:05:34] Retrying...
#> ℹ [2025-07-26 08:06:34] Error in `req_perform()`:
#> ℹ [2025-07-26 08:06:34] ! Failed to perform HTTP request.
#> ℹ [2025-07-26 08:06:34] Caused by error in `curl::curl_fetch_memory()`:
#> ℹ [2025-07-26 08:06:34] ! Timeout was reached [feb2021.archive.ensembl.org]:
#> ℹ [2025-07-26 08:06:34] Operation timed out after 60002 milliseconds with 0 bytes received
#> ℹ [2025-07-26 08:06:34]
#> ℹ [2025-07-26 08:06:34] Get errors when connecting with ensembl mart...
#> Error in log_message(out, message_type = "error"): Error in `req_perform()`: ! Failed to perform HTTP request. Caused by
#> error in `curl::curl_fetch_memory()`: ! Timeout was reached
#> [feb2021.archive.ensembl.org]: Operation timed out after 60002 milliseconds
#> with 0 bytes received
StatPlot(
GetFeaturesData(pancreas_sub, "RNA"),
stat.by = "TF",
group.by = "VerSeDa",
stat_type = "count",
plot_type = "bar",
position = "dodge",
label = TRUE,
NA_stat = FALSE
)
#> Error in log_message(paste0(i, " is not in the meta.data."), message_type = "error"): VerSeDa is not in the meta.data.