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Statistical plot of cells

Source: R/CellStatPlot.R
CellStatPlot.Rd

Statistical plot of cells

Usage

CellStatPlot(
  srt,
  stat.by,
  group.by = NULL,
  split.by = NULL,
  bg.by = NULL,
  cells = 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

srt

A Seurat object.

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.

cells

A character vector specifying the cells to include in the plot. Default is NULL.

flip

Whether to flip the plot. Default is FALSE.

NA_color

The color to use for missing values.

NA_stat

Whether to include missing values in the plot. Default is TRUE.

keep_empty

Whether to keep empty groups in the plot. Default is FALSE.

individual

Whether to plot individual groups separately. Default is FALSE.

stat_level

The level(s) of the variable(s) specified in stat.by to include in the plot. Default is NULL.

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

Whether to add labels on the plot. Default is FALSE.

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

Whether to combine multiple plots into a single plot. Default is TRUE.

nrow

The number of rows in the combined plot. Default is NULL.

ncol

The number of columns in the combined plot. Default is NULL.

byrow

Whether to fill the plot by row or by column. Default is TRUE.

force

Whether to force the plot even if some variables have more than 100 levels. Default is FALSE.

seed

The random seed to use for reproducible results. Default is 11.

See also

StatPlot

Examples

data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
#> 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 
p1 <- CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "SubCellType",
  label = TRUE
)
p1


thisplot::panel_fix(p1, height = 2, width = 3)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "SubCellType",
  stat_type = "count",
  position = "dodge",
  label = TRUE
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "SubCellType",
  bg.by = "CellType",
  palette = "Set1",
  stat_type = "count",
  position = "dodge"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  plot_type = "bar"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  plot_type = "rose"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  plot_type = "ring"
)
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_col()`).


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  plot_type = "pie"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  plot_type = "dot"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  plot_type = "bar"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  plot_type = "rose"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  plot_type = "ring"
)
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_col()`).


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  plot_type = "area"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  plot_type = "dot"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  plot_type = "trend"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  plot_type = "bar",
  individual = TRUE
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  stat_type = "count",
  plot_type = "bar"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  stat_type = "count",
  plot_type = "rose"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  stat_type = "count",
  plot_type = "ring"
)
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_col()`).


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  stat_type = "count",
  plot_type = "area"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  stat_type = "count",
  plot_type = "dot"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  stat_type = "count",
  plot_type = "trend"
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  stat_type = "count",
  plot_type = "bar",
  position = "dodge",
  label = TRUE
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  stat_type = "count",
  plot_type = "rose",
  position = "dodge",
  label = TRUE
)


CellStatPlot(
  pancreas_sub,
  stat.by = "Phase",
  group.by = "CellType",
  stat_type = "count",
  plot_type = "ring",
  position = "dodge",
  label = TRUE
)
#> 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()`).


CellStatPlot(
  pancreas_sub,
  stat.by = c("CellType", "Phase"),
  plot_type = "sankey"
)
#>  
#> → Will install 2 packages.
#> → All 2 packages (0 B) are cached.
#> + forcats    1.0.1     
#> + ggsankey   0.0.99999 [bld][cmp] (GitHub: b675d0d)
#> ✔ All system requirements are already installed.
#>   
#> ℹ No downloads are needed, 2 pkgs are cached
#> ✔ Got forcats 1.0.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (422.23 kB)
#> ✔ Got ggsankey 0.0.99999 (source) (277.80 kB)
#> ℹ Installing system requirements
#> ℹ Executing `sudo sh -c apt-get -y update`
#> Get:1 file:/etc/apt/apt-mirrors.txt Mirrorlist [144 B]
#> Hit:6 https://packages.microsoft.com/repos/azure-cli noble InRelease
#> Hit:7 https://packages.microsoft.com/ubuntu/24.04/prod noble InRelease
#> Hit:2 http://azure.archive.ubuntu.com/ubuntu noble InRelease
#> Hit:3 http://azure.archive.ubuntu.com/ubuntu noble-updates InRelease
#> Hit:4 http://azure.archive.ubuntu.com/ubuntu noble-backports InRelease
#> Hit:5 http://azure.archive.ubuntu.com/ubuntu noble-security InRelease
#> Reading package lists...
#> ℹ Executing `sudo sh -c apt-get -y install make libicu-dev`
#> Reading package lists...
#> Building dependency tree...
#> Reading state information...
#> make is already the newest version (4.3-4.1build2).
#> libicu-dev is already the newest version (74.2-1ubuntu3.1).
#> 0 upgraded, 0 newly installed, 0 to remove and 49 not upgraded.
#> ✔ Installed forcats 1.0.1  (1s)
#> ℹ Packaging ggsankey 0.0.99999
#> ✔ Packaged ggsankey 0.0.99999 (587ms)
#> ℹ Building ggsankey 0.0.99999
#> ✔ Built ggsankey 0.0.99999 (2.2s)
#> ✔ Installed ggsankey 0.0.99999 (github::davidsjoberg/ggsankey@b675d0d) (1s)
#> ✔ 1 pkg + 45 deps: kept 44, added 2, dld 2 (NA B) [9.3s]


CellStatPlot(
  pancreas_sub,
  stat.by = c("CellType", "Phase"),
  plot_type = "chord"
)


CellStatPlot(
  pancreas_sub,
  stat.by = c("CellType", "Phase"),
  plot_type = "venn",
  stat_level = list(
    CellType = c("Ductal", "Ngn3-low-EP"),
    Phase = "S"
  )
)
#>  
#> → Will install 8 packages.
#> → All 8 packages (0 B) are cached.
#> + admisc          0.39  
#> + aplot           0.2.9 
#> + ggVennDiagram   1.5.4 
#> + ggfun           0.2.0 
#> + ggplotify       0.1.3 
#> + gridGraphics    0.5-1 
#> + venn            1.12  
#> + yulab.utils     0.2.2 
#> ✔ All system requirements are already installed.
#>   
#> ℹ No downloads are needed, 8 pkgs are cached
#> ✔ Got yulab.utils 0.2.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (145.09 kB)
#> ✔ Got ggplotify 0.1.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (142.82 kB)
#> ✔ Got ggfun 0.2.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (250.63 kB)
#> ✔ Got admisc 0.39 (x86_64-pc-linux-gnu-ubuntu-24.04) (374.81 kB)
#> ✔ Got gridGraphics 0.5-1 (x86_64-pc-linux-gnu-ubuntu-24.04) (249.33 kB)
#> ✔ Got aplot 0.2.9 (x86_64-pc-linux-gnu-ubuntu-24.04) (105.37 kB)
#> ✔ Got venn 1.12 (x86_64-pc-linux-gnu-ubuntu-24.04) (308.02 kB)
#> ✔ Got ggVennDiagram 1.5.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (5.27 MB)
#> ℹ Installing system requirements
#> ℹ Executing `sudo sh -c apt-get -y update`
#> Get:1 file:/etc/apt/apt-mirrors.txt Mirrorlist [144 B]
#> Hit:2 http://azure.archive.ubuntu.com/ubuntu noble InRelease
#> Hit:3 http://azure.archive.ubuntu.com/ubuntu noble-updates InRelease
#> Hit:6 https://packages.microsoft.com/repos/azure-cli noble InRelease
#> Hit:4 http://azure.archive.ubuntu.com/ubuntu noble-backports InRelease
#> Hit:5 http://azure.archive.ubuntu.com/ubuntu noble-security InRelease
#> Hit:7 https://packages.microsoft.com/ubuntu/24.04/prod noble InRelease
#> Reading package lists...
#> ℹ Executing `sudo sh -c apt-get -y install libcurl4-openssl-dev libssl-dev make zlib1g-dev pandoc libicu-dev`
#> Reading package lists...
#> Building dependency tree...
#> Reading state information...
#> libcurl4-openssl-dev is already the newest version (8.5.0-2ubuntu10.6).
#> libssl-dev is already the newest version (3.0.13-0ubuntu3.6).
#> make is already the newest version (4.3-4.1build2).
#> zlib1g-dev is already the newest version (1:1.3.dfsg-3.1ubuntu2.1).
#> pandoc is already the newest version (3.1.3+ds-2).
#> libicu-dev is already the newest version (74.2-1ubuntu3.1).
#> 0 upgraded, 0 newly installed, 0 to remove and 49 not upgraded.
#> ✔ Installed admisc 0.39  (60ms)
#> ✔ Installed aplot 0.2.9  (75ms)
#> ✔ Installed ggfun 0.2.0  (134ms)
#> ✔ Installed ggplotify 0.1.3  (165ms)
#> ✔ Installed gridGraphics 0.5-1  (1s)
#> ✔ Installed ggVennDiagram 1.5.4  (1.1s)
#> ✔ Installed venn 1.12  (103ms)
#> ✔ Installed yulab.utils 0.2.2  (45ms)
#> ✔ 1 pkg + 90 deps: kept 83, added 8, dld 8 (6.85 MB) [7.3s]


pancreas_sub$Progenitor <- pancreas_sub$CellType %in% c("Ngn3-low-EP", "Ngn3-high-EP")
pancreas_sub$G2M <- pancreas_sub$Phase == "G2M"
pancreas_sub$Fancb_Expressed <- GetAssayData5(
  pancreas_sub,
  assay = "RNA",
  layer = "counts"
)["Fancb", ] > 0
pancreas_sub$Dlg3_Expressed <- GetAssayData5(
  pancreas_sub,
  assay = "RNA",
  layer = "counts"
)["Dlg3", ] > 0
CellStatPlot(
  pancreas_sub,
  stat.by = c(
    "Progenitor", "G2M", "Fancb_Expressed", "Dlg3_Expressed"
  ),
  plot_type = "venn",
  stat_level = "TRUE"
)


CellStatPlot(
  pancreas_sub,
  stat.by = c(
    "Progenitor", "G2M", "Fancb_Expressed", "Dlg3_Expressed"
  ),
  plot_type = "upset",
  stat_level = "TRUE"
)
#>  
#> → Will install 1 package.
#> → The package (0 B) is cached.
#> + ggupset   0.4.1 
#> ✔ All system requirements are already installed.
#>   
#> ℹ No downloads are needed, 1 pkg is cached
#> ✔ Got ggupset 0.4.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.59 MB)
#> ℹ Installing system requirements
#> ℹ Executing `sudo sh -c apt-get -y update`
#> Get:1 file:/etc/apt/apt-mirrors.txt Mirrorlist [144 B]
#> Hit:2 http://azure.archive.ubuntu.com/ubuntu noble InRelease
#> Hit:6 https://packages.microsoft.com/repos/azure-cli noble InRelease
#> Hit:3 http://azure.archive.ubuntu.com/ubuntu noble-updates InRelease
#> Hit:7 https://packages.microsoft.com/ubuntu/24.04/prod noble InRelease
#> Hit:4 http://azure.archive.ubuntu.com/ubuntu noble-backports InRelease
#> Hit:5 http://azure.archive.ubuntu.com/ubuntu noble-security InRelease
#> Reading package lists...
#> ℹ Executing `sudo sh -c apt-get -y install make`
#> Reading package lists...
#> Building dependency tree...
#> Reading state information...
#> make is already the newest version (4.3-4.1build2).
#> 0 upgraded, 0 newly installed, 0 to remove and 49 not upgraded.
#> ✔ Installed ggupset 0.4.1  (38ms)
#> ✔ 1 pkg + 37 deps: kept 37, added 1, dld 1 (2.59 MB) [4.1s]
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the ggupset package.
#>   Please report the issue at <https://github.com/const-ae/ggupset/issues>.


sum(
  pancreas_sub$Progenitor == "FALSE" &
    pancreas_sub$G2M == "FALSE" &
    pancreas_sub$Fancb_Expressed == "TRUE" &
    pancreas_sub$Dlg3_Expressed == "FALSE"
)
#> [1] 6