Closed GoBucket closed 1 year ago
dbdimitrov
commented
1 year ago Hi,
You need to provide a group_col that is present within your sce object. In the example, stim is the one that corresponds to the condition (i.e. whether the samples are stimulated or not).
Hope this helps.
GoBucket
commented
1 year ago Hi,
In my dataset, stim is present in the object.
I have checked via colData(sce)
GoBucket
commented
1 year ago I have found the fix.
Turns out I had to
sce$context <- paste(sce$stim, sep="|")
and then sample_col = "context", for liana_bysample
What I did before was sample_col = "stim",
Thank you for your help and prompt replies.
Hi, When I try to run
plot_c2c_overview(sce, group_col="stim")I get the following error:
Error indplyr::select(): ! Can't subset columns that don't exist. x Columncontextdoesn't exist. Runrlang::last_error()to see where the error occurred.I have ran glimpse(factors) which showed:
List of 4 $ contexts : tibble [2 x 9] (S3: tbl_df/tbl/data.frame) ..$ context : Factor w/ 2 levels "24H","48H": 1 2 ..$ Factor.1: num [1:2] 0.662 0.75 ..$ Factor.2: num [1:2] 0.774 0.633 ..$ Factor.3: num [1:2] 0.657 0.754 ..$ Factor.4: num [1:2] 0.702 0.712 ..$ Factor.5: num [1:2] 0.685 0.729 ..$ Factor.6: num [1:2] 0.882 0.471 ..$ Factor.7: num [1:2] 0.71 0.704 ..$ Factor.8: num [1:2] 0.44 0.898 ..- attr(*, "pandas.index")=Index(['24H', '48H'], dtype='object') $ interactions: tibble [2,893 x 9] (S3: tbl_df/tbl/data.frame) ..$ lr : Factor w/ 2893 levels "A2M^LRP1","ACE^BDKRB2",..: 1 2 3 4 5 6 7 8 9 10 ... ..$ Factor.1: num [1:2893] 2.07e-05 8.69e-21 5.91e-02 2.37e-02 3.38e-03 ... ..$ Factor.2: num [1:2893] 0.01851 0.00308 0.03423 0.06876 0.02213 ... ..$ Factor.3: num [1:2893] 1.11e-28 1.02e-05 1.73e-02 1.93e-02 1.34e-02 ... ..$ Factor.4: num [1:2893] 4.57e-12 5.20e-03 3.16e-02 2.73e-02 1.37e-02 ... ..$ Factor.5: num [1:2893] 0.0884 0.00566 0.02742 0.02388 0.00333 ... ..$ Factor.6: num [1:2893] 1.87e-02 1.32e-04 5.52e-02 3.09e-02 2.59e-19 ... ..$ Factor.7: num [1:2893] 1.26e-02 5.98e-34 4.43e-02 3.63e-02 1.00e-02 ... ..$ Factor.8: num [1:2893] 1.05e-02 9.74e-23 2.64e-02 5.23e-02 2.16e-03 ... ..- attr(*, "pandas.index")=Index(['A2M^LRP1', 'ACE^BDKRB2', 'ACTR2^ADRB2', 'ACTR2^LDLR', 'ADAM10^AXL', 'ADAM10^CADM1', 'ADAM10^CD44', 'ADAM10^GPNMB', 'ADAM10^MET', 'ADAM10^NOTCH1', ... 'WNT9A^FZD7_LRP6', 'WNT9A^FZD8_LRP5', 'WNT9A^FZD8_LRP6', 'WNT9A^FZD9_LRP5', 'WNT9A^FZD9_LRP6', 'XCL1^ADGRV1', 'XCL1^XCR1', 'YBX1^NOTCH1', 'ZP3^EGFR', 'ZP3^MERTK'], dtype='object', length=2893) $ senders : tibble [7 x 9] (S3: tbl_df/tbl/data.frame) ..$ celltype: Factor w/ 7 levels "Dopaminergic neurons",..: 1 2 3 4 5 6 7 ..$ Factor.1: num [1:7] 0.428 0.427 0.231 0.284 0.338 ... ..$ Factor.2: num [1:7] 0.432 0.421 0.261 0.328 0.3 ... ..$ Factor.3: num [1:7] 0.02812 0.03798 0.00116 0.00233 0.99739 ... ..$ Factor.4: num [1:7] 0.4 0.374 0.347 0.345 0.401 ... ..$ Factor.5: num [1:7] 0.0232 0.0338 0.0577 0.9805 0.1827 ... ..$ Factor.6: num [1:7] 0.43 0.434 0.212 0.315 0.304 ... ..$ Factor.7: num [1:7] 0.2529 0.1286 0.9315 0.0634 0.0681 ... ..$ Factor.8: num [1:7] 0.48 0.401 0.304 0.256 0.203 ... ..- attr(*, "pandas.index")=Index(['Dopaminergic neurons', 'Immune system cells', 'Microglial cells', 'Neural Progenitor cells', 'Oligodendrocytes', 'Radial glial cells', 'Unknown'], dtype='object') $ receivers : tibble [7 x 9] (S3: tbl_df/tbl/data.frame) ..$ celltype: Factor w/ 7 levels "Dopaminergic neurons",..: 1 2 3 4 5 6 7 ..$ Factor.1: num [1:7] 0.2916 0.6959 0.4426 0.1017 0.0309 ... ..$ Factor.2: num [1:7] 0.5042 0.1627 0.0145 0.058 0.1654 ... ..$ Factor.3: num [1:7] 0.399 0.316 0.403 0.392 0.387 ... ..$ Factor.4: num [1:7] 0.0218 0.0783 0.0472 0.0317 0.9928 ... ..$ Factor.5: num [1:7] 0.386 0.347 0.413 0.384 0.375 ... ..$ Factor.6: num [1:7] 0.25473 0.00679 0.63078 0.6129 0.38802 ... ..$ Factor.7: num [1:7] 0.4 0.365 0.434 0.354 0.325 ... ..$ Factor.8: num [1:7] 0.268 0.17 0.206 0.768 0.399 ... ..- attr(*, "pandas.index")=Index(['Dopaminergic neurons', 'Immune system cells', 'Microglial cells', 'Neural Progenitor cells', 'Oligodendrocytes', 'Radial glial cells', 'Unknown'], dtype='object')Any help is much appreciated thank you!