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welch-lab / liger

R package for integrating and analyzing multiple single-cell datasets
GNU General Public License v3.0
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PBMC Vignette Plotting Issue #188

Closed taekb closed 3 years ago

taekb commented 4 years ago

I am following the PBMC alignment vignette, and I am experiencing a rather bizarre issue at the t-SNE plotting step where all of the labels come out as hexadecimals and are just unreadable.

example_tsne_plot

When I check the axis.labels slots, etc., the actual values stored there are indeed the character vectors that I was expecting to see, but the plot for some reason fails to print them out in a readable format. Can someone help point out where the problem may reside in?

For your reference, I am running and visualizing the code on a Jupyter notebook loaded with an IRkernel, which does often seem to have its own set of problems. Also, here is a summary of the values that are stored in my ggplot object:


 $ data       :'data.frame':    6332 obs. of  4 variables:
  ..$ tsne1  : num [1:6332] 29.93 -9.31 40.57 -15.94 14.9 ...
  ..$ tsne2  : num [1:6332] 5.26 5.86 7.38 12.31 23.01 ...
  ..$ Dataset: chr [1:6332] "tenx" "seqwell" "tenx" "seqwell" ...
  ..$ Cluster: Factor w/ 22 levels "1","10","11",..: 13 15 2 11 8 1 2 4 12 11 ...
 $ layers     :List of 1
  ..$ :Classes 'LayerInstance', 'Layer', 'ggproto', 'gg' <ggproto object: Class LayerInstance, Layer, gg>
    aes_params: list
    compute_aesthetics: function
    compute_geom_1: function
    compute_geom_2: function
    compute_position: function
    compute_statistic: function
    data: waiver
    draw_geom: function
    finish_statistics: function
    geom: <ggproto object: Class GeomPoint, Geom, gg>
        aesthetics: function
        default_aes: uneval
        draw_group: function
        draw_key: function
        draw_layer: function
        draw_panel: function
        extra_params: na.rm
        handle_na: function
        non_missing_aes: size shape colour
        optional_aes: 
        parameters: function
        required_aes: x y
        setup_data: function
        setup_params: function
        use_defaults: function
        super:  <ggproto object: Class Geom, gg>
    geom_params: list
    inherit.aes: TRUE
    layer_data: function
    map_statistic: function
    mapping: NULL
    position: <ggproto object: Class PositionIdentity, Position, gg>
        compute_layer: function
        compute_panel: function
        required_aes: 
        setup_data: function
        setup_params: function
        super:  <ggproto object: Class Position, gg>
    print: function
    setup_layer: function
    show.legend: NA
    stat: <ggproto object: Class StatIdentity, Stat, gg>
        aesthetics: function
        compute_group: function
        compute_layer: function
        compute_panel: function
        default_aes: uneval
        extra_params: na.rm
        finish_layer: function
        non_missing_aes: 
        optional_aes: 
        parameters: function
        required_aes: 
        retransform: TRUE
        setup_data: function
        setup_params: function
        super:  <ggproto object: Class Stat, gg>
    stat_params: list
    super:  <ggproto object: Class Layer, gg> 
 $ scales     :Classes 'ScalesList', 'ggproto', 'gg' <ggproto object: Class ScalesList, gg>
    add: function
    clone: function
    find: function
    get_scales: function
    has_scale: function
    input: function
    n: function
    non_position_scales: function
    scales: list
    super:  <ggproto object: Class ScalesList, gg> 
 $ mapping    :List of 3
  ..$ colour: language ~Dataset
  .. ..- attr(*, ".Environment")=<environment: 0x55bf680af338> 
  ..$ x     : language ~tsne1
  .. ..- attr(*, ".Environment")=<environment: 0x55bf680af338> 
  ..$ y     : language ~tsne2
  .. ..- attr(*, ".Environment")=<environment: 0x55bf680af338> 
  ..- attr(*, "class")= chr "uneval"
 $ theme      :List of 93
  ..$ line                      :List of 6
  .. ..$ colour       : chr "black"
  .. ..$ size         : num 0.5
  .. ..$ linetype     : num 1
  .. ..$ lineend      : chr "butt"
  .. ..$ arrow        : logi FALSE
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_line" "element"
  ..$ rect                      :List of 5
  .. ..$ fill         : logi NA
  .. ..$ colour       : logi NA
  .. ..$ size         : num 0.5
  .. ..$ linetype     : num 1
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_rect" "element"
  ..$ text                      :List of 11
  .. ..$ family       : chr ""
  .. ..$ face         : chr "plain"
  .. ..$ colour       : chr "black"
  .. ..$ size         : num 12
  .. ..$ hjust        : num 0.5
  .. ..$ vjust        : num 0.5
  .. ..$ angle        : num 0
  .. ..$ lineheight   : num 0.9
  .. ..$ margin       : 'margin' num [1:4] 0pt 0pt 0pt 0pt
  .. .. ..- attr(*, "valid.unit")= int 8
  .. .. ..- attr(*, "unit")= chr "pt"
  .. ..$ debug        : logi FALSE
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_text" "element"
  ..$ title                     : NULL
  ..$ aspect.ratio              : NULL
  ..$ axis.title                : NULL
  ..$ axis.title.x              :List of 11
  .. ..$ family       : NULL
  .. ..$ face         : NULL
  .. ..$ colour       : NULL
  .. ..$ size         : NULL
  .. ..$ hjust        : NULL
  .. ..$ vjust        : num 1
  .. ..$ angle        : NULL
  .. ..$ lineheight   : NULL
  .. ..$ margin       : 'margin' num [1:4] 3pt 0pt 0pt 0pt
  .. .. ..- attr(*, "valid.unit")= int 8
  .. .. ..- attr(*, "unit")= chr "pt"
  .. ..$ debug        : NULL
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_text" "element"
  ..$ axis.title.x.top          :List of 11
  .. ..$ family       : NULL
  .. ..$ face         : NULL
  .. ..$ colour       : NULL
  .. ..$ size         : NULL
  .. ..$ hjust        : NULL
  .. ..$ vjust        : num 0
  .. ..$ angle        : NULL
  .. ..$ lineheight   : NULL
  .. ..$ margin       : 'margin' num [1:4] 0pt 0pt 3pt 0pt
  .. .. ..- attr(*, "valid.unit")= int 8
  .. .. ..- attr(*, "unit")= chr "pt"
  .. ..$ debug        : NULL
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_text" "element"
  ..$ axis.title.x.bottom       : NULL
  ..$ axis.title.y              :List of 11
  .. ..$ family       : NULL
  .. ..$ face         : NULL
  .. ..$ colour       : NULL
  .. ..$ size         : NULL
  .. ..$ hjust        : NULL
  .. ..$ vjust        : num 1
  .. ..$ angle        : num 90
  .. ..$ lineheight   : NULL
  .. ..$ margin       : 'margin' num [1:4] 0pt 3pt 0pt 0pt
  .. .. ..- attr(*, "valid.unit")= int 8
  .. .. ..- attr(*, "unit")= chr "pt"
  .. ..$ debug        : NULL
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_text" "element"
  ..$ axis.title.y.left         : NULL
  ..$ axis.title.y.right        :List of 11
  .. ..$ family       : NULL
  .. ..$ face         : NULL
  .. ..$ colour       : NULL
  .. ..$ size         : NULL
  .. ..$ hjust        : NULL
  .. ..$ vjust        : num 0
  .. ..$ angle        : num -90
  .. ..$ lineheight   : NULL
  .. ..$ margin       : 'margin' num [1:4] 0pt 0pt 0pt 3pt
  .. .. ..- attr(*, "valid.unit")= int 8
  .. .. ..- attr(*, "unit")= chr "pt"
  .. ..$ debug        : NULL
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_text" "element"
  ..$ axis.text                 :List of 11
  .. ..$ family       : NULL
  .. ..$ face         : NULL
  .. ..$ colour       : chr "black"
  .. ..$ size         : num 10.3
  .. ..$ hjust        : NULL
  .. ..$ vjust        : NULL
  .. ..$ angle        : NULL
  .. ..$ lineheight   : NULL
  .. ..$ margin       : NULL
  .. ..$ debug        : NULL
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_text" "element"
  ..$ axis.text.x               :List of 11
  .. ..$ family       : NULL
  .. ..$ face         : NULL
  .. ..$ colour       : NULL
  .. ..$ size         : NULL
  .. ..$ hjust        : NULL
  .. ..$ vjust        : num 1
  .. ..$ angle        : NULL
  .. ..$ lineheight   : NULL
  .. ..$ margin       : 'margin' num [1:4] 2.57pt 0pt 0pt 0pt
  .. .. ..- attr(*, "valid.unit")= int 8
  .. .. ..- attr(*, "unit")= chr "pt"
  .. ..$ debug        : NULL
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_text" "element"
  ..$ axis.text.x.top           :List of 11
  .. ..$ family       : NULL
  .. ..$ face         : NULL
  .. ..$ colour       : NULL
  .. ..$ size         : NULL
  .. ..$ hjust        : NULL
  .. ..$ vjust        : num 0
  .. ..$ angle        : NULL
  .. ..$ lineheight   : NULL
  .. ..$ margin       : 'margin' num [1:4] 0pt 0pt 2.57pt 0pt
  .. .. ..- attr(*, "valid.unit")= int 8
  .. .. ..- attr(*, "unit")= chr "pt"
  .. ..$ debug        : NULL
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_text" "element"
  ..$ axis.text.x.bottom        : NULL
  ..$ axis.text.y               :List of 11
  .. ..$ family       : NULL
  .. ..$ face         : NULL
  .. ..$ colour       : NULL
  .. ..$ size         : NULL
  .. ..$ hjust        : num 1
  .. ..$ vjust        : NULL
  .. ..$ angle        : NULL
  .. ..$ lineheight   : NULL
  .. ..$ margin       : 'margin' num [1:4] 0pt 2.57pt 0pt 0pt
  .. .. ..- attr(*, "valid.unit")= int 8
  .. .. ..- attr(*, "unit")= chr "pt"
  .. ..$ debug        : NULL
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_text" "element"
  ..$ axis.text.y.left          : NULL
  ..$ axis.text.y.right         :List of 11
  .. ..$ family       : NULL
  .. ..$ face         : NULL
  .. ..$ colour       : NULL
  .. ..$ size         : NULL
  .. ..$ hjust        : num 0
  .. ..$ vjust        : NULL
  .. ..$ angle        : NULL
  .. ..$ lineheight   : NULL
  .. ..$ margin       : 'margin' num [1:4] 0pt 0pt 0pt 2.57pt
  .. .. ..- attr(*, "valid.unit")= int 8
  .. .. ..- attr(*, "unit")= chr "pt"
  .. ..$ debug        : NULL
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_text" "element"
  ..$ axis.ticks                :List of 6
  .. ..$ colour       : chr "black"
  .. ..$ size         : num 0.5
  .. ..$ linetype     : NULL
  .. ..$ lineend      : NULL
  .. ..$ arrow        : logi FALSE
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_line" "element"
  ..$ axis.ticks.x              : NULL
  ..$ axis.ticks.x.top          : NULL
  ..$ axis.ticks.x.bottom       : NULL
  ..$ axis.ticks.y              : NULL
  ..$ axis.ticks.y.left         : NULL
  ..$ axis.ticks.y.right        : NULL
  ..$ axis.ticks.length         : 'unit' num 3pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ axis.ticks.length.x       : NULL
  ..$ axis.ticks.length.x.top   : NULL
  ..$ axis.ticks.length.x.bottom: NULL
  ..$ axis.ticks.length.y       : NULL
  ..$ axis.ticks.length.y.left  : NULL
  ..$ axis.ticks.length.y.right : NULL
  ..$ axis.line                 :List of 6
  .. ..$ colour       : chr "black"
  .. ..$ size         : num 0.5
  .. ..$ linetype     : NULL
  .. ..$ lineend      : chr "square"
  .. ..$ arrow        : logi FALSE
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_line" "element"
  ..$ axis.line.x               : NULL
  ..$ axis.line.x.top           : NULL
  ..$ axis.line.x.bottom        : NULL
  ..$ axis.line.y               : NULL
  ..$ axis.line.y.left          : NULL
  ..$ axis.line.y.right         : NULL
  ..$ legend.background         : list()
  .. ..- attr(*, "class")= chr [1:2] "element_blank" "element"
  ..$ legend.margin             : 'margin' num [1:4] 0pt 0pt 0pt 0pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ legend.spacing            : 'unit' num 12pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ legend.spacing.x          : NULL
  ..$ legend.spacing.y          : NULL
  ..$ legend.key                : list()
  .. ..- attr(*, "class")= chr [1:2] "element_blank" "element"
  ..$ legend.key.size           : 'unit' num 13.2pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ legend.key.height         : NULL
  ..$ legend.key.width          : NULL
  ..$ legend.text               :List of 11
  .. ..$ family       : NULL
  .. ..$ face         : NULL
  .. ..$ colour       : NULL
  .. ..$ size         : 'rel' num 0.857
  .. ..$ hjust        : NULL
  .. ..$ vjust        : NULL
  .. ..$ angle        : NULL
  .. ..$ lineheight   : NULL
  .. ..$ margin       : NULL
  .. ..$ debug        : NULL
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_text" "element"
  ..$ legend.text.align         : NULL
  ..$ legend.title              :List of 11
  .. ..$ family       : NULL
  .. ..$ face         : NULL
  .. ..$ colour       : NULL
  .. ..$ size         : NULL
  .. ..$ hjust        : num 0
  .. ..$ vjust        : NULL
  .. ..$ angle        : NULL
  .. ..$ lineheight   : NULL
  .. ..$ margin       : NULL
  .. ..$ debug        : NULL
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_text" "element"
  ..$ legend.title.align        : NULL
  ..$ legend.position           : chr "right"
  ..$ legend.direction          : NULL
  ..$ legend.justification      : chr [1:2] "left" "center"
  ..$ legend.box                : NULL
  ..$ legend.box.just           : NULL
  ..$ legend.box.margin         : 'margin' num [1:4] 0pt 0pt 0pt 0pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ legend.box.background     : list()
  .. ..- attr(*, "class")= chr [1:2] "element_blank" "element"
  ..$ legend.box.spacing        : 'unit' num 12pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ panel.background          : list()
  .. ..- attr(*, "class")= chr [1:2] "element_blank" "element"
  ..$ panel.border              : list()
  .. ..- attr(*, "class")= chr [1:2] "element_blank" "element"
  ..$ panel.spacing             : 'unit' num 6pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ panel.spacing.x           : NULL
  ..$ panel.spacing.y           : NULL
  ..$ panel.grid                : list()
  .. ..- attr(*, "class")= chr [1:2] "element_blank" "element"
  ..$ panel.grid.major          : NULL
  ..$ panel.grid.minor          : NULL
  ..$ panel.grid.major.x        : NULL
  ..$ panel.grid.major.y        : NULL
  ..$ panel.grid.minor.x        : NULL
  ..$ panel.grid.minor.y        : NULL
  ..$ panel.ontop               : logi FALSE
  ..$ plot.background           : list()
  .. ..- attr(*, "class")= chr [1:2] "element_blank" "element"
  ..$ plot.title                :List of 11
  .. ..$ family       : NULL
  .. ..$ face         : chr "bold"
  .. ..$ colour       : NULL
  .. ..$ size         : 'rel' num 1.14
  .. ..$ hjust        : num 0
  .. ..$ vjust        : num 1
  .. ..$ angle        : NULL
  .. ..$ lineheight   : NULL
  .. ..$ margin       : 'margin' num [1:4] 0pt 0pt 6pt 0pt
  .. .. ..- attr(*, "valid.unit")= int 8
  .. .. ..- attr(*, "unit")= chr "pt"
  .. ..$ debug        : NULL
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_text" "element"
  ..$ plot.title.position       : chr "panel"
  ..$ plot.subtitle             :List of 11
  .. ..$ family       : NULL
  .. ..$ face         : NULL
  .. ..$ colour       : NULL
  .. ..$ size         : 'rel' num 0.857
  .. ..$ hjust        : num 0
  .. ..$ vjust        : num 1
  .. ..$ angle        : NULL
  .. ..$ lineheight   : NULL
  .. ..$ margin       : 'margin' num [1:4] 0pt 0pt 6pt 0pt
  .. .. ..- attr(*, "valid.unit")= int 8
  .. .. ..- attr(*, "unit")= chr "pt"
  .. ..$ debug        : NULL
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_text" "element"
  ..$ plot.caption              :List of 11
  .. ..$ family       : NULL
  .. ..$ face         : NULL
  .. ..$ colour       : NULL
  .. ..$ size         : 'rel' num 0.786
  .. ..$ hjust        : num 1
  .. ..$ vjust        : num 1
  .. ..$ angle        : NULL
  .. ..$ lineheight   : NULL
  .. ..$ margin       : 'margin' num [1:4] 6pt 0pt 0pt 0pt
  .. .. ..- attr(*, "valid.unit")= int 8
  .. .. ..- attr(*, "unit")= chr "pt"
  .. ..$ debug        : NULL
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_text" "element"
  ..$ plot.caption.position     : chr "panel"
  ..$ plot.tag                  :List of 11
  .. ..$ family       : NULL
  .. ..$ face         : chr "bold"
  .. ..$ colour       : NULL
  .. ..$ size         : NULL
  .. ..$ hjust        : num 0
  .. ..$ vjust        : num 0.7
  .. ..$ angle        : NULL
  .. ..$ lineheight   : NULL
  .. ..$ margin       : NULL
  .. ..$ debug        : NULL
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_text" "element"
  ..$ plot.tag.position         : num [1:2] 0 1
  ..$ plot.margin               : 'margin' num [1:4] 6pt 6pt 6pt 6pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ strip.background          :List of 5
  .. ..$ fill         : chr "grey80"
  .. ..$ colour       : NULL
  .. ..$ size         : NULL
  .. ..$ linetype     : NULL
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_rect" "element"
  ..$ strip.background.x        : NULL
  ..$ strip.background.y        : NULL
  ..$ strip.placement           : chr "inside"
  ..$ strip.text                :List of 11
  .. ..$ family       : NULL
  .. ..$ face         : NULL
  .. ..$ colour       : NULL
  .. ..$ size         : 'rel' num 0.857
  .. ..$ hjust        : NULL
  .. ..$ vjust        : NULL
  .. ..$ angle        : NULL
  .. ..$ lineheight   : NULL
  .. ..$ margin       : 'margin' num [1:4] 3pt 3pt 3pt 3pt
  .. .. ..- attr(*, "valid.unit")= int 8
  .. .. ..- attr(*, "unit")= chr "pt"
  .. ..$ debug        : NULL
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_text" "element"
  ..$ strip.text.x              : NULL
  ..$ strip.text.y              :List of 11
  .. ..$ family       : NULL
  .. ..$ face         : NULL
  .. ..$ colour       : NULL
  .. ..$ size         : NULL
  .. ..$ hjust        : NULL
  .. ..$ vjust        : NULL
  .. ..$ angle        : num -90
  .. ..$ lineheight   : NULL
  .. ..$ margin       : NULL
  .. ..$ debug        : NULL
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_text" "element"
  ..$ strip.switch.pad.grid     : 'unit' num 3pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ strip.switch.pad.wrap     : 'unit' num 3pt
  .. ..- attr(*, "valid.unit")= int 8
  .. ..- attr(*, "unit")= chr "pt"
  ..$ strip.text.y.left         :List of 11
  .. ..$ family       : NULL
  .. ..$ face         : NULL
  .. ..$ colour       : NULL
  .. ..$ size         : NULL
  .. ..$ hjust        : NULL
  .. ..$ vjust        : NULL
  .. ..$ angle        : num 90
  .. ..$ lineheight   : NULL
  .. ..$ margin       : NULL
  .. ..$ debug        : NULL
  .. ..$ inherit.blank: logi TRUE
  .. ..- attr(*, "class")= chr [1:2] "element_text" "element"
  ..- attr(*, "class")= chr [1:2] "theme" "gg"
  ..- attr(*, "complete")= logi TRUE
  ..- attr(*, "validate")= logi TRUE
 $ coordinates:Classes 'CoordCartesian', 'Coord', 'ggproto', 'gg' <ggproto object: Class CoordCartesian, Coord, gg>
    aspect: function
    backtransform_range: function
    clip: on
    default: TRUE
    distance: function
    expand: TRUE
    is_free: function
    is_linear: function
    labels: function
    limits: list
    modify_scales: function
    range: function
    render_axis_h: function
    render_axis_v: function
    render_bg: function
    render_fg: function
    setup_data: function
    setup_layout: function
    setup_panel_guides: function
    setup_panel_params: function
    setup_params: function
    train_panel_guides: function
    transform: function
    super:  <ggproto object: Class CoordCartesian, Coord, gg> 
 $ facet      :Classes 'FacetNull', 'Facet', 'ggproto', 'gg' <ggproto object: Class FacetNull, Facet, gg>
    compute_layout: function
    draw_back: function
    draw_front: function
    draw_labels: function
    draw_panels: function
    finish_data: function
    init_scales: function
    map_data: function
    params: list
    setup_data: function
    setup_params: function
    shrink: TRUE
    train_scales: function
    vars: function
    super:  <ggproto object: Class FacetNull, Facet, gg> 
 $ plot_env   :<environment: 0x55bf680af338> 
 $ labels     :List of 4
  ..$ y     : chr "tSNE2"
  ..$ x     : chr "tSNE1"
  ..$ title : chr "PBMC Example"
  ..$ colour: chr "Dataset"
 $ guides     :List of 1
  ..$ colour:List of 21
  .. ..$ title         : list()
  .. .. ..- attr(*, "class")= chr "waiver"
  .. ..$ title.position: NULL
  .. ..$ title.theme   : NULL
  .. ..$ title.hjust   : NULL
  .. ..$ title.vjust   : NULL
  .. ..$ label         : logi TRUE
  .. ..$ label.position: NULL
  .. ..$ label.theme   : NULL
  .. ..$ label.hjust   : NULL
  .. ..$ label.vjust   : NULL
  .. ..$ keywidth      : NULL
  .. ..$ keyheight     : NULL
  .. ..$ direction     : NULL
  .. ..$ override.aes  :List of 1
  .. .. ..$ size: num 5
  .. ..$ nrow          : NULL
  .. ..$ ncol          : NULL
  .. ..$ byrow         : logi FALSE
  .. ..$ reverse       : logi FALSE
  .. ..$ order         : num 0
  .. ..$ available_aes : chr "any"
  .. ..$ name          : chr "legend"
  .. ..- attr(*, "class")= chr [1:2] "guide" "legend"
 - attr(*, "class")= chr [1:2] "gg" "ggplot"
​```
skpalan commented 4 years ago

What are the actual commands you used for plotting? Can you try setting the axis labels manually? For example, plotByDatasetAndCluster(liger_object, axis.labels = c("TSNE_1", "TSNE_2")).

skpalan commented 3 years ago

Closed for now. Feel free to open a new issue if you have any updates!