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.dataspecifying the variable(s) to be plotted.- group.by
The column name in
meta.dataspecifying the grouping variable.- split.by
The column name in
meta.dataspecifying the splitting variable.- bg.by
The column name in
meta.dataspecifying 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.byto 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)
pancreas_sub <- standard_scop(pancreas_sub)
#> ℹ [2025-09-20 13:59:00] Start standard scop workflow...
#> ℹ [2025-09-20 13:59:01] Checking a list of <Seurat> object...
#> ! [2025-09-20 13:59:01] Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2025-09-20 13:59:01] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on the data 1/1 of the `srt_list`...
#> ℹ [2025-09-20 13:59:03] Perform `Seurat::FindVariableFeatures()` on the data 1/1 of the `srt_list`...
#> ℹ [2025-09-20 13:59:04] Use the separate HVF from srt_list
#> ℹ [2025-09-20 13:59:04] Number of available HVF: 2000
#> ℹ [2025-09-20 13:59:04] Finished check
#> ℹ [2025-09-20 13:59:04] Perform `Seurat::ScaleData()`
#> Warning: Different features in new layer data than already exists for scale.data
#> ℹ [2025-09-20 13:59:04] Perform pca linear dimension reduction
#> StandardPC_ 1
#> Positive: Aplp1, Cpe, Gnas, Fam183b, Map1b, Hmgn3, Pcsk1n, Chga, Tuba1a, Bex2
#> Syt13, Isl1, 1700086L19Rik, Pax6, Chgb, Scgn, Rbp4, Scg3, Gch1, Camk2n1
#> Cryba2, Pcsk2, Pyy, Tspan7, Mafb, Hist3h2ba, Dbpht2, Abcc8, Rap1b, Slc38a5
#> Negative: Spp1, Anxa2, Sparc, Dbi, 1700011H14Rik, Wfdc2, Gsta3, Adamts1, Clu, Mgst1
#> Bicc1, Ldha, Vim, Cldn3, Cyr61, Rps2, Mt1, Ptn, Phgdh, Nudt19
#> Smtnl2, Smco4, Habp2, Mt2, Col18a1, Rpl12, Galk1, Cldn10, Acot1, Ccnd1
#> StandardPC_ 2
#> Positive: Rbp4, Tagln2, Tuba1b, Fkbp2, Pyy, Pcsk2, Iapp, Tmem27, Meis2, Tubb4b
#> Pcsk1n, Dbpht2, Rap1b, Dynll1, Tubb2a, Sdf2l1, Scgn, 1700086L19Rik, Scg2, Abcc8
#> Atp1b1, Hspa5, Fam183b, Papss2, Slc38a5, Scg3, Mageh1, Tspan7, Ppp1r1a, Ociad2
#> Negative: Neurog3, Btbd17, Gadd45a, Ppp1r14a, Neurod2, Sox4, Smarcd2, Mdk, Pax4, Btg2
#> Sult2b1, Hes6, Grasp, Igfbpl1, Gpx2, Cbfa2t3, Foxa3, Shf, Mfng, Tmsb4x
#> Amotl2, Gdpd1, Cdc14b, Epb42, Rcor2, Cotl1, Upk3bl, Rbfox3, Cldn6, Cer1
#> StandardPC_ 3
#> Positive: Nusap1, Top2a, Birc5, Aurkb, Cdca8, Pbk, Mki67, Tpx2, Plk1, Ccnb1
#> 2810417H13Rik, Incenp, Cenpf, Ccna2, Prc1, Racgap1, Cdk1, Aurka, Cdca3, Hmmr
#> Spc24, Kif23, Sgol1, Cenpe, Cdc20, Hist1h1b, Cdca2, Mxd3, Kif22, Ska1
#> Negative: Anxa5, Pdzk1ip1, Acot1, Tpm1, Anxa2, Dcdc2a, Capg, Sparc, Ttr, Pamr1
#> Clu, Cxcl12, Ndrg2, Hnf1aos1, Gas6, Gsta3, Krt18, Ces1d, Atp1b1, Muc1
#> Hhex, Acadm, Spp1, Enpp2, Bcl2l14, Sat1, Smtnl2, 1700011H14Rik, Tgm2, Fam159a
#> StandardPC_ 4
#> Positive: Glud1, Tm4sf4, Akr1c19, Cldn4, Runx1t1, Fev, Pou3f4, Gm43861, Pgrmc1, Arx
#> Cd200, Lrpprc, Hmgn3, Ppp1r14c, Pam, Etv1, Tsc22d1, Slc25a5, Akap17b, Pgf
#> Fam43a, Emb, Jun, Krt8, Dnajc12, Mid1ip1, Ids, Rgs17, Uchl1, Alcam
#> Negative: Ins2, Ins1, Ppp1r1a, Nnat, Calr, Sytl4, Sdf2l1, Iapp, Pdia6, Mapt
#> G6pc2, C2cd4b, Npy, Gng12, P2ry1, Ero1lb, Adra2a, Papss2, Arhgap36, Fam151a
#> Dlk1, Creld2, Gip, Tmem215, Gm27033, Cntfr, Prss53, C2cd4a, Lyve1, Ociad2
#> StandardPC_ 5
#> Positive: Pdx1, Nkx6-1, Npepl1, Cldn4, Cryba2, Fev, Jun, Chgb, Gng12, Adra2a
#> Mnx1, Sytl4, Pdk3, Gm27033, Nnat, Chga, Ins2, 1110012L19Rik, Enho, Krt7
#> Mlxipl, Tmsb10, Flrt1, Pax4, Tubb3, Prrg2, Gars, Frzb, BC023829, Gm2694
#> Negative: Irx2, Irx1, Gcg, Ctxn2, Tmem27, Ctsz, Tmsb15l, Nap1l5, Pou6f2, Gria2
#> Ghrl, Peg10, Smarca1, Arx, Lrpap1, Rgs4, Ttr, Gast, Tmsb15b2, Serpina1b
#> Slc16a10, Wnk3, Ly6e, Auts2, Sct, Arg1, Dusp10, Sphkap, Dock11, Edn3
#> ℹ [2025-09-20 13:59:05] Perform `Seurat::FindClusters()` with louvain and `cluster_resolution` = 0.6
#> ℹ [2025-09-20 13:59:05] Reorder clusters...
#> ! [2025-09-20 13:59:05] Using `Seurat::AggregateExpression()` to calculate pseudo-bulk data for <Assay5>
#> ℹ [2025-09-20 13:59:06] Perform umap nonlinear dimension reduction
#> ℹ [2025-09-20 13:59:06] Non-linear dimensionality reduction (umap) using (Standardpca) dims (1-50) as input
#> ℹ [2025-09-20 13:59:06] UMAP will return its model
#> ℹ [2025-09-20 13:59:10] Non-linear dimensionality reduction (umap) using (Standardpca) dims (1-50) as input
#> ℹ [2025-09-20 13:59:10] UMAP will return its model
#> ✔ [2025-09-20 13:59:14] Run scop standard workflow done
head(pancreas_sub@meta.data)
#> orig.ident nCount_RNA nFeature_RNA S_score G2M_score
#> AAACCTGAGCCTTGAT SeuratProject 7071 2613 -0.01470664 -0.2326104
#> AAACCTGGTAAGTGGC SeuratProject 5026 2211 -0.17998111 -0.1260295
#> AAACGGGAGATATGGT SeuratProject 6194 2486 -0.16794573 -0.1666881
#> AAACGGGCAAAGAATC SeuratProject 6370 2581 -0.17434505 -0.2216024
#> AAACGGGGTACAGTTC SeuratProject 9182 2906 -0.18656224 -0.1571970
#> AAACGGGTCAGCTCTC SeuratProject 5892 2282 -0.12347911 -0.2298337
#> nCount_spliced nFeature_spliced nCount_unspliced
#> AAACCTGAGCCTTGAT 7071 2613 953
#> AAACCTGGTAAGTGGC 5026 2211 1000
#> AAACGGGAGATATGGT 6194 2486 721
#> AAACGGGCAAAGAATC 6370 2581 1544
#> AAACGGGGTACAGTTC 9182 2906 2262
#> AAACGGGTCAGCTCTC 5892 2282 935
#> nFeature_unspliced CellType SubCellType Phase
#> AAACCTGAGCCTTGAT 638 Ductal Ductal G1
#> AAACCTGGTAAGTGGC 623 Ngn3-high-EP Ngn3-high-EP G1
#> AAACGGGAGATATGGT 550 Ductal Ductal G1
#> AAACGGGCAAAGAATC 1015 Endocrine Beta G1
#> AAACGGGGTACAGTTC 1096 Endocrine Beta G1
#> AAACGGGTCAGCTCTC 712 Ngn3-low-EP Ngn3-low-EP G1
#> Standardpca_SNN_res.0.6 ident Standardpcaclusters
#> AAACCTGAGCCTTGAT 0 <NA> <NA>
#> AAACCTGGTAAGTGGC 3 <NA> <NA>
#> AAACGGGAGATATGGT 0 <NA> <NA>
#> AAACGGGCAAAGAATC 1 <NA> <NA>
#> AAACGGGGTACAGTTC 1 <NA> <NA>
#> AAACGGGTCAGCTCTC 0 <NA> <NA>
#> Standardclusters
#> AAACCTGAGCCTTGAT <NA>
#> AAACCTGGTAAGTGGC <NA>
#> AAACGGGAGATATGGT <NA>
#> AAACGGGCAAAGAATC <NA>
#> AAACGGGGTACAGTTC <NA>
#> AAACGGGTCAGCTCTC <NA>
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("CSPA", "TF")
)
#> ℹ [2025-09-20 13:59:15] Species: Mus_musculus
#> ℹ [2025-09-20 13:59:15] Preparing database: TF
#> ℹ [2025-09-20 13:59:17] Error in utils::download.file(url = url, destfile = destfile, method = method, : cannot open URL 'https://guolab.wchscu.cn/AnimalTFDB4_static/download/TF_list_final/Mus_musculus_TF'
#> ! [2025-09-20 13:59:17] Failed to download using auto, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/TF_list_final/Mus_musculus_TF>
#> ℹ [2025-09-20 13:59:19] Error in utils::download.file(url = url, destfile = destfile, method = method, : 'wget' call had nonzero exit status
#> ! [2025-09-20 13:59:19] Failed to download using wget, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/TF_list_final/Mus_musculus_TF>
#> ℹ [2025-09-20 13:59:21] Error in utils::download.file(url = url, destfile = destfile, method = method, : cannot open URL 'https://guolab.wchscu.cn/AnimalTFDB4_static/download/TF_list_final/Mus_musculus_TF'
#> ! [2025-09-20 13:59:21] Failed to download using libcurl, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/TF_list_final/Mus_musculus_TF>
#> Warning: incomplete final line found by readTableHeader on '/tmp/Rtmp8qFX1m/file266a73d8b579'
#> ℹ [2025-09-20 13:59:25] Error in utils::download.file(url = url, destfile = destfile, method = method, : cannot open URL 'https://guolab.wchscu.cn/AnimalTFDB4_static/download/Cof_list_final/Mus_musculus_Cof'
#> ! [2025-09-20 13:59:25] Failed to download using auto, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/Cof_list_final/Mus_musculus_Cof>
#> ℹ [2025-09-20 13:59:27] Error in utils::download.file(url = url, destfile = destfile, method = method, : 'wget' call had nonzero exit status
#> ! [2025-09-20 13:59:27] Failed to download using wget, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/Cof_list_final/Mus_musculus_Cof>
#> ℹ [2025-09-20 13:59:29] Error in utils::download.file(url = url, destfile = destfile, method = method, : cannot open URL 'https://guolab.wchscu.cn/AnimalTFDB4_static/download/Cof_list_final/Mus_musculus_Cof'
#> ! [2025-09-20 13:59:29] Failed to download using libcurl, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/Cof_list_final/Mus_musculus_Cof>
#> Warning: incomplete final line found by readTableHeader on '/tmp/Rtmp8qFX1m/file266a73d8b579'
#> ! [2025-09-20 13:59:31] Use the human annotation to create the TF database for Mus_musculus
#> ℹ [2025-09-20 13:59:32] Error in utils::download.file(url = url, destfile = destfile, method = method, : cannot open URL 'https://guolab.wchscu.cn/AnimalTFDB4_static/download/TF_list_final/Homo_sapiens_TF'
#> ! [2025-09-20 13:59:32] Failed to download using auto, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/TF_list_final/Homo_sapiens_TF>
#> ℹ [2025-09-20 13:59:34] Error in utils::download.file(url = url, destfile = destfile, method = method, : 'wget' call had nonzero exit status
#> ! [2025-09-20 13:59:34] Failed to download using wget, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/TF_list_final/Homo_sapiens_TF>
#> ℹ [2025-09-20 13:59:36] Error in utils::download.file(url = url, destfile = destfile, method = method, : cannot open URL 'https://guolab.wchscu.cn/AnimalTFDB4_static/download/TF_list_final/Homo_sapiens_TF'
#> ! [2025-09-20 13:59:36] Failed to download using libcurl, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/TF_list_final/Homo_sapiens_TF>
#> Warning: incomplete final line found by readTableHeader on '/tmp/Rtmp8qFX1m/file266a73d8b579'
#> ℹ [2025-09-20 13:59:39] Error in utils::download.file(url = url, destfile = destfile, method = method, : cannot open URL 'https://guolab.wchscu.cn/AnimalTFDB4_static/download/Cof_list_final/Homo_sapiens_Cof'
#> ! [2025-09-20 13:59:39] Failed to download using auto, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/Cof_list_final/Homo_sapiens_Cof>
#> ℹ [2025-09-20 13:59:41] Error in utils::download.file(url = url, destfile = destfile, method = method, : 'wget' call had nonzero exit status
#> ! [2025-09-20 13:59:41] Failed to download using wget, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/Cof_list_final/Homo_sapiens_Cof>
#> ℹ [2025-09-20 13:59:43] Error in utils::download.file(url = url, destfile = destfile, method = method, : cannot open URL 'https://guolab.wchscu.cn/AnimalTFDB4_static/download/Cof_list_final/Homo_sapiens_Cof'
#> ! [2025-09-20 13:59:43] Failed to download using libcurl, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/Cof_list_final/Homo_sapiens_Cof>
#> Warning: incomplete final line found by readTableHeader on '/tmp/Rtmp8qFX1m/file266a73d8b579'
#> Error in data.frame(Term = "TF", symbol = tf[["Symbol"]]): arguments imply differing number of rows: 1, 0
StatPlot(
GetFeaturesData(pancreas_sub, "RNA"),
stat.by = "TF",
group.by = "CSPA",
stat_type = "count",
plot_type = "bar",
position = "dodge",
label = TRUE,
NA_stat = FALSE
)
#> Error in StatPlot(GetFeaturesData(pancreas_sub, "RNA"), stat.by = "TF", group.by = "CSPA", stat_type = "count", plot_type = "bar", position = "dodge", label = TRUE, NA_stat = FALSE): CSPA is not in the meta.data.