Babyplots Jupyter Notebook Demo

Babyplots is available through the babyplots python package to use in jupyter notebooks to visualize your data.

In [2]:
from babyplots import Babyplot
import pandas as pd

Plot Demo

In [3]:
dat = pd.read_csv("E:/Dokumente/repos/mca_dt.txt", sep="\t")
In [4]:
dat.head()
Out[4]:
UMAP_1 UMAP_2 UMAP_3 orig.ident nCount_RNA nFeature_RNA ClusterID Tissue Batch Cell.Barcode percent.mt RNA_snn_res.3 seurat_clusters
0 2.232274 -7.775582 -10.968533 MouseCellAtlas 11512 3469 Bladder_9 Bladder Bladder_1 CCATCTAGCGAGTTTAGG 2.936067 69 69
1 2.092620 -7.915526 -10.998805 MouseCellAtlas 13580 3725 Bladder_9 Bladder Bladder_1 GAGGAGCGCTTGATACAG 2.260677 69 69
2 1.947722 -7.657710 -10.638845 MouseCellAtlas 12089 3401 Bladder_9 Bladder Bladder_1 CCAGACACAATAGAATTA 2.225163 69 69
3 2.109386 -7.830964 -10.924024 MouseCellAtlas 12949 3574 Bladder_9 Bladder Bladder_1 CCGACGGGACATATGGCG 1.814812 69 69
4 2.229176 -7.529998 -10.927272 MouseCellAtlas 11790 3392 Bladder_9 Bladder Bladder_1 TAGCATTCAAAGATTCCA 2.044105 69 69
In [5]:
coords = dat.iloc[:,0:3].values.tolist()
In [6]:
clusts = dat["Tissue"].values.tolist()
In [7]:
bp = Babyplot()
bp.add_plot(coords, "pointCloud", "categories", clusts, {"colorScale": "Paired"})
In [8]:
bp
Out[8]:
In [9]:
bp.width = "768px"
bp.height = "320px"
In [10]:
bp.plots[0]["options"]["colorScale"]  = "Set3"
bp.plots[0]["options"]["showLegend"] = False
bp.plots[0]["options"]["showAxes"] = [True, True, True]
In [11]:
bp
Out[11]:

Image Stack Demo

In [12]:
bp2 = Babyplot(background_color="#000000ff")
bp2.add_tiff("RGB.tif", channel_thresholds=[0.3,0.1, 1], options={"size": 1, "intensityMode": "alpha"})
In [13]:
bp2.plots[0]["attributes"]
Out[13]:
{'dim': [1024, 1024, 3, 98]}
In [14]:
bp2.plots[0]["plot_type"]
Out[14]:
'imageStack'
In [15]:
bp2
Out[15]:

Iris PCA example

In [16]:
import numpy as np
from sklearn import decomposition
from sklearn import datasets
np.random.seed(5)
In [17]:
iris = datasets.load_iris()
X = iris.data
y = iris.target
In [18]:
pca = decomposition.PCA(n_components=3)
pca.fit(X)
X = pca.transform(X)
In [19]:
bp_iris = Babyplot(background_color="#262626ff", x_scale=0.6)

bp_iris.add_plot(X.tolist(), "shapeCloud", "categories", y.tolist(), {"shape": "sphere", "colorScale": "Set2", "showAxes": [True, True, True], "axisLabels": ["PC 1", "PC 2", "PC 3"]})
In [22]:
bp_iris
Out[22]:
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